Does he still count as a Christian? I know David Barton tries to claim him. Of course, Barton makes up fictional quotes, too.
As a Christian (a fundy no less), and far be it from me to judge the heart of an individual man, but from what I've read and know of Jefferson I would say, no, he was not a Christian, nor was America founded as a "Christian" nation, although Christian teachings, the Bible, and principles were the majority rule at the time (i.e. most accepted these facts at the time, thus they controlled the laws, norms, customs, ect).