First off let me preface by saying I realize and acknowledge that it is extremely difficult to evenly compare the limited data we have on TB v JfN. That said, here we go with my best effort.
Josh was, above all else, a warrior. I would say that on paper Timmy takes the trophy, but the intangibles Josh brought are really hard to ignore. That said, TB also steps up and commands the offense with a sense of dominance that made you feel confident 4th and goal on the 2 was going our way.
The other element is the supporting cast around him, JfN and TB excel with the right blend of Wide outs, A&B Backs and OL, and the reality is their requirements aren't for the same.
If I was forced to pick my favorite, it is JfN (due mainly to the many memories of him bulldozing and ball snatching us back to victory) but if I had to pick the best QB to win with a team like we had this year it is Timmy for the ability to pass.