I got the impression that he voted for Obama in 2008 from The Guardian interview. He attributed Obama's election as the reason why he didn't go public at the time.
I'm admittedly projecting from his remarks, so it isn't necessarily accurate. I don't recall him stating that he voted for a third party candidate, however.
From an earlier Guardian article:
http://www.guardian.co.uk/world/2013/jun/09/nsa-whistleblower-edward-snowden-why
“A lot of people in 2008 voted for Obama. I did not vote for him. I voted for a third party.