I don't think it is quite as stark as apples to oranges yet certainly not easy to make a just comparison. I'd put it this way, if you had to have one tandem or the other at the QB and Coach positions, which tandem would you choose: Brady and Dungy or Manning and BB? As vaulted a position Brady holds in my football view, I'd take BB and Manning.
But if you're trying to compare QB to QB, if you want to win, as other posters pointed out, Brady is the choice. He has shown a greater ability to get it done in the playoffs. However, I think it is also fair to say if you are looking for QB to put the pass where it needs to be most frequently, from my own observation, Manning has shown a greater ability to do that.
Lastly, I think it is fair to say that Indy and the Patriots are spoiled. The vast majority of fans watch their team's QB play inconsistently year in and year out.