Close close call. Politcally speaking, John is much more aware and his questions are always meaningful and make sense, unlike Stephen's which are most of the times just to make fun of his guest! However, its undenaible that Stephen is a better performer overall and in terms of the comic factor, ranks much higher than John.
So if your looking for a good fun laugh, while the host interviews a good array of guests, while actually understanding the points they are trying to raise, and ofcourse the hilarious bits, then John is your man. If on the other hand you want to just laugh, while the host takes the mickey out of everything that moves, and more importantly his guests, with a surprising twist every now and then, then Colbert is your man.
I chose Colbert! I just love his arrogance!