Peyton Manning has the luxury of playing half of his games in a dome where his stats won't be affected the weather. Fact is Manning never wins when he plays in the snow. Watch numerous playoff games for evidence. On the other hand, Brady plays a decent number of games in cold, snowy Foxborough.
Also, Manning had some excellent receivers for years while Brady waited until 2007 to get an elite receivers in Moss and Welker. Even then he still threw to about 10 different guys while Manning mainly stuck with Harrision and Wayne. Also, did you remember how explosive Brady's stats were that year when he finally got good receivers? Imagine if he had them most of his career like Manning.
Brady came out of nowhere off the bench for Bledsoe and took the Patriots right to the Super Bowl while it took Manning years into his career. Brady went to 4 Super Bowls and won 3 while Manning went to 2 Super Bowls and won one. At the end of the day, that stat matters the most.
Both are Hall of Fame QBs though nonetheless. It's like comparing Marino to Montana.