Just speaking for my self, I do think that Jon Stewart is more entertaining to watch that Stephen Colbert. Others may disagree, but I think that he has better jokes and hits better punch lines that Colbert. They are both very popular comedians though and are very popular on tv.
Yes, I think that Jon Stewart is a better comedian than Stephen Colbert, because Jon Stewart's wit is more versatile. Stephen Colbert mostly has the same theme that he does over and over again. Both of them have comedic timing, but Jon Stewart has a bigger variety of material. He is just more talented overall.
While I do like Stephen Colbert's brand of humor and satire, I find that the Colbert Report is a little too one note for my tastes. Jon Stewart's humor, delivery and interviewing style all add up to make him a slightly better comedian than Colbert. Fortunately, we can watch them both every night.
I personally prefer Jon Stewart, I find his jokes funnier than Stephen Colbert's, but overall it is a very subjective decision. People could easily side either way and no one would be particularly wrong in this situation so its not a particularly good debate question, in my opinion. People could prefer one or the other for several reasons.
Jon Stewart is without doubt a very funny man with comic genius and his political sense is amazing. But I am a fan of Stephen Colbert's wider range of facial expressions and gestures and the fact that he so ironically plays the part of a conservative political pundit on his show.