Completion Percentage, Passer rating, and Adjusted Yards/Attempt (passing yards + 20*passing TD - 45*interceptions)/(passes attempted)
Home: 63.0%, 94.2, 7.36
Away: 63.7%, 92.5, 7.28
Home: 65.3%, 98.9, 7.94
Away: 64.3%, 91.6, 7.17
Home: 65.4%, 94.7, 7.40
Away: 64.1%, 89.0, 6.88
Why does this matter? Because Manning has played all of his home games in Indianapolis' dome, while Brees has split his games between New Orleans' Dome and the oh-so-blustery San Diego outdoor stadium.
Brady has played all of his home games outdoors in frigid New England.
Now look at the away statistics:
Brady Away: 63.7%, 92.5, 7.28
Manning Away: 64.3%, 91.6, 7.17
Brees Away: 64.1%, 89.0, 6.88
The only place you can fault Brady is his completion percentage... until 2007, Brady's receivers were worse than anything Manning or Brees has ever had. I can't find statistics, but I'm fairly certain that if you count WR drops (which are an official statistic, just hard to find), Brady would be equal or better to Manning and Brees.
Now lets look at comebacks and game winning drives:
Brady: 21 Fourth Quarter Comebacks, 29 Game Winning Drives, 126 regular season games started, 50 with a 7 or fewer point margin
Manning: 35 Fourth quarter comebacks, 44 Game Winning Drives, 192 regular season games started, 88 with a 7 or fewer point margin
Brees: 11 Fourth Quarter Comebacks, 18 Game Winning Drives, 122 regular season games started, 54 with a 7 or fewer point margin
to convert these to rates:
Brady: led comebacks in 42.0% of close games, led game winning drives in 58% of close games
Manning: led comebacks in 39.8% of close games, led game winning drives in 50% of close games
Brees: led comebacks in 20.4% of close games, led game winning drives in 33.3% of close games
Of course, I understand this isnt the greatest statistical instrument for "clutchness", given that close games could be "winning" or "losing" varieties, and defense matters, and it doesn't count "putting your opponents away" by pulling more than one touchdown away from an opponent near the end of a game, but seeing as the only statistics I have are those available on pro-football-reference.com, this will have to be a proxy for clutch. Again, Brady has the edge, followed by Manning, with Brees way behind.
Brady: 2007. 50 TD (1st all time), 4806 yards (3rd all time), 8 int, 117.2 rating (2nd all time). 68.9% completions, 9.4 adjusted yards/attempt
Manning: 2004. 49 TD (2nd all time), 4557 yards, 10 int, 121.1 rating (1st all time), 67.6% completions, 10.2 adjusted yards/attempt
Brees: 2009. 34 TD, 4388 yards, 11 int, 109.6 rating. 70.6% completions, 8.9 adjusted yards/attempt
Again, Brees falls short. Manning vs Brady's best seasons are fairly comparable, with Brady leading in TD, yards, ints and completion %, and Manning leading in rating and adjusted yards per attempt.
Now to the playoffs - record
Brady: 14-4, 3 rings
Manning: 9-9, 1 ring
Brees: 4-2, 1 ring
I don't have playoff statistics, because I can't find them, but given the small sample of games, the outcomes and performances, it's a safe bet that Manning comes behind Brady and Brees (I don't know what the stats are for Brady and Brees, but Brees seems to be out of this debate already).
Can we finally put this "who is the best QB in the game" argument to rest?