Q: Was Freud the first to make the connection between monotheism and Aten?
There are a couple of uncertainties encapsulated in this question.
If you want to know which Western researcher first discovered that Akhenaten's religious reform in Egypt was "somehow" monotheistic: we have to observe that there are just a few stations in the discovery: 1714 Claude Sicard finds a stele in Amarna, 1799 Napoleon brings Egypt's past into fashion among European researchers, 1826 John Gardner Wilkinson and James Burton visit the place and document it, 1828 Champollion visits the place for just one day, 1845 Karl Bunsen publishes 3 volumes covering Egypt's place in world history, but then already
Karl Richard Lepsius wrote about that what you might want to know in 1851. "Über den ersten Aegyptischen Götterkreis und seine geschichtlich-mythologische Entstehung. Akademie der Wissenschaften, Berlin 1851." Although he thinks in that work that Akhenaten is a priest of Re and only that there are strong tendencies towards monotheism recognisable.
If you want to know whether Freud was the first of anything in relating what we might call monotheism in ancient Egypt to monotheism in ancient Israel? Then the answer is that Freud was bold enough to speculate that Moses was himself an Egyptian, not an Israelite or Hebrew, bold enough to muse the idea that Moses was eventually killed by the Hebrews for his radicalism. Freud was a keen observer of Egyptology for half a century and entertained ideas in that fashion for the entire time. For as soon as the efforts of exclusiveness in Akhenaten's religious reforms became apparent in scholarship speculations ran wild to connect it to Jewish history.
Apart from the obvious differences and distinctions between religious traditions, the parallels between the religious history of Egypt, Israel and other near Eastern belief systems are at least as interesting. But this is not really an invention of Western, modern scholars.
The monotheist revolution of Akhenaten and the founding of Israelite monotheism by Moses have often been brought together, most famously by Sigmund Freud in his last book, Moses and Monotheism. Chapter 4, “Moses and Akhenaten: Memory and History,” investigates the historical and mnemohistorical foundations of this problematic rapprochement. Akhenaten is a figure exclusively of history who was denied any tradition and memory in ancient Egyptian culture, having been subjected to a complete damnatio memoriae. Moses, on the other hand, is a figure exclusively of memory, accruing an immense importance as the founding father of monotheism in the Jewish, Christian, and Islamic traditions, of whose historical existence, however, not the least traces have been found. It is, therefore, small wonder that the two figures, complementing each other in such a perfect way, have often been brought together.
There is, however, even a late Egyptian tradition identifying Akhenaten (called Osarseph) with Moses: Manetho’s legend of the lepers, whose reference to the Amarna experience is corroborated by a passage in Diodorus on the pyramids. These and other sources show that there was a strong tradition in Egyptian cultural memory about three great catastrophes and times of suffering in the past and their triumphant overcoming, the Amarna experience being one of them. These traditions concerning Egyptian suffering and final triumph show striking parallels to the Biblical story of the Exodus that point to the fact that the Late Egyptian tradition (ca. 600 BCE onward) about Akhenaten–Osarseph and the Biblical tradition about Moses and the Exodus did not arise completely independently of each other.
Jan Assmann: "From Akhenaten to Moses. Ancient Egypt and Religious Change", The American University in Cairo Press: Cairo, New York, 2014, p 3.
Freud did indeed land a few "firsts" with his book. But most of these firsts are now as criticised as they were when he published his book. Although few of the points that are not entirely psychoanalytical but actually grounded in the understanding of history from his day, are unique, the composition and synthesis of ideas certainly is. That Moses bears an Egyptian name and that this might hint at him being ethnically Egyptian is a hypothesis that is even still current in catholic theology seminars.
But for the "connection" between Moses and Akhenaten, Freud was just by far not the first on that. So I would conclude, equal in boldness to Freud, as soon as anyone identified Akhenaten as some kind of monotheist, everyone started to see the "connection" to what eventually became Jewish monotheism immediately.
Since the early 20th century, scholars have posited that there was some possible connection between Akhenaten and ancient Israelite religion, Moses and monotheism.
James K. Hoffmeier: "Akhenaten and the Origins of Monotheism", Oxford University Press: Oxford, New York, 2014, p xi.
Q: Was Freud the first to say that Judaism borrowed from Atenism?
Most probably not.
Given that Freud published the famous book in 1939 and started to write it in 1937 I would request further precision from the OP as to the exact date that Freud first publicly entertained the idea. If we take 1937/9 as the cut-off date, this would be one earlier example:
H. R. Hall: "Egypt and the External World in the Time of Akhenaten", The Journal of Egyptian Archaeology, Vol. 7, No. 1/2 (Apr., 1921), pp. 39-53
It is however by no means impossible that its inspiration was not lost outside Egypt. In Nubia, where temples were erected to the Aten, it died; but in Palestine we cannot be certain that this was absolutely the case. Even in the midst of rebellion, a Palestinian Khinatuni seems to have been set up, as would naturally be expected from Egyptian officialism in the northern as in the southern external dominion; this would be entirely agreeable to the king: he would not fight, but he would teach. How do we know that the monotheistic doctrine of Heliopolis (again, Moses' "Wisdom of the Egyptians," learnt at On) did not survive at Khinatuni, whether that was at Jerusalem itself or possibly at Bethshemesh, " the House of the Sun," and that it was not the germ from which sprang the monotheism of the Hebrews, of ourselves, and of the Muslims ?
And even earlier, but focussing more on Joseph than Moses, but denying any uniqueness to monotheist thought in the old oriental context:
Hugo Winckler: "Abraham als Babylonier, Joseph als Ägypter: Der Weltgeschichtliche Hintergrund der Biblischen Vätergeschichten auf Grund der Keilinschriften", JC Hinrichs: Berlin, 1904. (Online at archive.org)
It has turned out that the historical personalities of this time were also known to the biblical tradition and that they are the ones to be assumed in an important episode of pre-Israelite history.
Amenophis IV, the Pharaoh to whom most of these letters are addressed, has Palestine ruled by a deputy at that time, a viceroy or whatever one wants to call him.
The decisive reason why the Joseph narrative must presuppose the conditions of this time, however, is not in the correspondence of the external conditions, but in the essence of the intention of the biblical narratives in general. Their purpose is to prove how and under what circumstances religion has developed, as the bearer of which the people of Israel feels. The essence of this religion is monotheism. For no one who has an insight into the essence of the Oriental cultural world, it is a question of whether thoughts such as those underlying the Mosaic doctrine were already thought by human heads in the millennia before Israel's existence as a people. This is also not the contradiction that this Israelite teaching itself wants to teach. Whoever claims this as Israel's merit, has the implementation of the monotheism contrary to the new Babylonian doctrine in the Hammurabi period originated - that is, inspired and conditioned by it, how every expression of human spiritual activity is stimulated by the world of thought of its time and determined in its development, how the Reformation received its impulses through grievances of the Catholic Church - in Egypt once an attempt was made to carry out a likewise monotheistic teaching, but "a new Pharaoh arose who knew nothing of Joseph", Egypt returned to its old gods.
(translation and emphasis mine)
In effect the whole paper that contains the last quote claims that monotheism was a near eastern development that spread through the whole region, with evidence of certain steps here and there, but Amenophis IV being just one salient step of a direct line, or branch, towards Israelite monotheism.
Let's approach this from the rear end of the horse and look at how Freud got his most inspiration from whom and how he differed from that direct inspiration:
Sigmund’s cryptic, phrase-a-day diary for that date merely mentions the visit of a “Mrs Gunn with Egyptian antiquity”, but he and his grandsons were documented inspecting goldfish in the garden pond in an amateur film by Princess Marie Bonaparte, now shown daily at the Freud Museum. A year later Lucian went to Cedric Morris’s East Anglian art school and, shortly after that, at around the time of his grandfather’s death, he was given the copy of Breasted’s Geschichte Aegyptens with which he posed for the Auerbach photograph half a century later. The distinctive recumbent manner in which Lucian poses so many of his sitters suggests the conscious or unconscious influence both of his grandfather’s psychoanalytical couch and of the Egyptian mummy, his dreaming figures, clothed or nude, staring into space until brought back to health and/or consciousness. The particular application of this supine pose to freaks, friends, wives, mistresses and mother alike (the latter depicted following her suicide attempt and eventually, mummy-like, in death itself), tends to support this hypothesis.
In Moses and Monotheism, Sigmund Freud went further than Breasted’s Dawn of Conscience to argue that Moses was an Egyptian who derived his iconoclastic monotheism from the revolutionary, sun-worshipping pharaoh, Akhenaten, and was then murdered by the ungrateful Jews he had led out of slavery. The book was completed in London and published in the last months of Freud’s life. Freud followed Breasted in believing that: “Our moral heritage...derives from a wider human past enormously older than the Hebrews, and it come to us through rather than from them.” Breasted had drawn attention to the striking parallels between Akhenaten’s “Hymn to the Sun” and Psalm 104, as well as the indebtedness of the Book of Proverbs to the so-called “Wisdom of Amenemope”.
Maurizio Ascari &, Adriana Corrado (Eds): "Sites of Exchange: European Crossroads and Faultlines", Rodopi: Amsterdam, 2006, p 45.