Thomas ususally gets the nod, because he got stuck with the nickname, Doubting Thomas. But all he did was want better ID of this new body Jesus. Yes the holes in his body helped quell the doubts.
But Peter. Peter was out walking on the freaking top of the water! I think he saw Jesus and said hey can I come on over, and even though he actually doin it, he freaked out, got afraid, doubted he could really do it and started to sink.
My vote goes to Peter as the Greatest Doubter, my hero...oompa