Massacres of Armenians in the Ottoman Empire goes back to at least 1894, but they increased during WWI. What is referred to as the Armenian Genocide is however sometimes limited to the events that happened during the mass deportation of Armenians in 1915-1916. The deportations ended in March 1916, and this ended the main part of the Armenian genocide, but anti-Armenian policy did not stop, and there was massacres of Armenians after this point as well.
Mustafa Kemal Atatürk was during WWI a military man, and was during the deportations in charge of first the 19th Division and the the XVI Army Corps, busy defending the western end of the Empire. As a leading officer he surely would have been aware of the deportations, but did not order them or participate in them, and I can find no evidence that he was involved in any of the massacres before the deportations either.
Atatürk was the leader of the Turkish Independence War, and as such nominally responsible for massacres during this period. However, he blamed the Turkish people and it's "excited state".
As he was a turk-nationalist and started a policy of oppressing and Turkifying minorities, it is quite likely that he supported the anti-Armenian policies. In August 1921 his nationalists took several Britons hostage (I've seen the numbers 22 and 29) and then made an exchange for the Turks that was detained for their involvement in the genocide.
The conclusion of this is that Atatürk is not to blame for the Genocide and does not have seem to be directly involved in either the deportations, nor the massacres. However, he does not seem to have opposed them, and possibly supported them. He certainly did nothing to stop them, even after he came to power.