Josephus writes that the Temple of Onias (Chonyo) in Egypt was built in Heliopoils, however the Talmud (Menahot 109b) seems to understand that the temple was built in Alexandria, not in Heliopolis?
The Talmud says that Onias fled "to Alexandria in Egypt", and "there he built an altar":
הלך לאלכסנדריא של מצרים ובנה שם מזבח
We may take שם "there" as reference to "Alexandria", but it may also reference "Egypt". IMHO, the second version is corroborated by the citation of Isaiah 19:19 in Menahot 109b:
ביום ההוא יהיה מזבח לה' בתוך ארץ מצרים ומצבה אצל גבולה לה
19In that day there will be an altar to the Lord in the heart of Egypt, and a monument to the Lord at its border.
Not to mention the disputes about Isaiah 19:18 (!), regarding the "City of Destruction" (עיר ההרס), maybe the "City of the Sun" (עיר החרס) -> Heliopolis (as in the "New International Version") or the "City of the Lion" -> Leontopolis:
18In that day five cities in Egypt will speak the language of Canaan and swear allegiance to the Lord Almighty. One of them will be called the City of Destruction (alternative reading: City of the Sun / City of the Lion).
As far as I see, the archaeological evidence doesn't help much. In 1905, Flinders Petrie claimed to have discovered the location of the Temple of Onias near Leontopolis (Tel el-Yehudiyah, see the Jewish Encyclopedia on the Temple of Onias), but as far as I can see, this is hotly contested. Among the resources available online, see Taylor, "A Second Temple in Egypt: the Evidence for the Zadokite Temple of Onias", esp. the last chapter on the Location of the Temple.
Another possible location of the Temple of Onias is Tell Basta (Bubastis). See G. Hata, "Where is The Temple Site of Onias IV in Egypt?", in: "Flavius Josephus : Interpretation and History", Leiden 2011, pp. 177-192.