It's a pretty simple answer.
Brady, and it's not even close. Stats do matter, but wins matter more.
13 of Manning's regular season 75 losses were his rookie year on a terrible team. In fact, 32 of those losses were in his first 4 years on a Colts's team with a lousy defense (average of #22 in points allowed).
Since then he's had a winning percentage of 76.6% (141-43) compared to Brady's career of 77.5% (155-45) with vastly better defenses - the Patriots under Brady never ranked lower than #17 in points allowed. 10 times Brady had a top 10 defense - Peyton only 6 (5 with the Colts and 1 with the Broncos).
Brady is lucky as hell to have been drafted by Belichick's Patriots.
Some numbers:
Games under 24 points given up:
Manning - 141-18 (.887) (2 losses in first season on Colts would be .898)
Brady - 134-13 (.912)
Game of 24+ points given up:
Manning - 43-69 (.384) (11 losses in first season on Colts would be .425)
Brady - 39-41 (.488)
Times scoring more than 24+ points:
Manning - 166 of 272 (61%)
Brady - 139 of 228 (61%)
Average points allowed by team:
Manning - 21.5
Brady - 18.8
If the team does give up 24 points what is the average they normally give up:
Manning - 30.7 (6% more PPG given up when allowing 24+ points)
Brady - 28.9
Numbers show these two are very very close. When you consider after throwing out Manning's rookie season vs
Brady coming into a playoff contender its just ever so slight of a margin.
Again I see both as pretty much equal, if I had a bad team I was trying to turn around I would take Manning in his prime. If I had a good team who just kept falling short I would take Brady in his prime. I feel that Bellichek plays a lot into Brady's success but since I dont know for sure you gotta think Brady just has better ability to deal with the spotlight of big games.