Manning had a higher QBR in the playoffs up until last year, maybe even now. Personally, i think Brady has one big advantage, he doesn't overthink as much as Manning. Manning's biggest flaw is that he is sometimes overthinking the game.
I rate Brady higher than Manning at the moment, but if Manning would be able to win another superbowl, i'm pretty sure most expert would rate him higher than Brady. Brady is great, don't get me wrong, but he wasn't nearly the player early in his career that he is now.
His peak from 2005 till 2009 was much more impressive to me than his early years, even though he couldn't win another Super Bowl. Also, if Brady manages to win another one with this roster this year, or next year, i will rate him as 2nd all-time below Montana, and another MVP would probably seal it for him.
A couple factors to consider.
People talk about how Brady won his Super Bowls as though it was the defense. They tend to forget that in the Carolina Super Bowl, the defense gave up 29 points in 30 minutes. Brady put up a top 5 all-time Super Bowl yardage performance. He slung the ball all over the field. What kills me when people take credit away from Brady is that they say it was Vinatieri who was the key in the those Super Bowls. It's like they didn't even watch. Vinatieri missed two chippy field goals against Carolina. If he had had a normal Vinatieri day, the game doesn't even come down to the final seconds.
On Montana, why do people give Montana credit for losing more than Brady in the conference playoffs? He's undefeated in SBs, but he lost a lot more before the SBs.
A couple factors to hang your hat on.
1. The Brady of pre-2007 didn't have offensive weapons like Harrison, Wayne, Moss and Welker. He was throwing to Jermaine Wiggins, Deion Branch, David Patten, Reche Caldwell, David Givens, Jabar Gaffney, Donte Stallworth, etc. Only Troy Brown qualkifies as a special player. So it's no wonder Brady looked better later.
2. QBR and even qb rating are flawed for me. Brady's best year ever was last year. He controlled that offense and had it operating like a well-oiled machine. What floored me in stat analysis is that the pundits had Aaron Rodgers up there last year while Brady was down. The Patriots scored 36 points a game. Packers 28. The Patriots converted 50% of 3rd downs. Packers below 40%. The Patriots had 24 rushing TDs. The Packers 7. Countless times, Brady got them to the red zone, and they jammed the ball in running on short yardage. Brady had 4 rushing TDs himself. For me, QB rating and QBR are fantasy stats. The NFL Network fantasy show actually said Brady had a rough game last week (he threw one TD and the final interception against Carolina). Ridiculous, he had a great game.
3. Manning has higher ratings overall. BUT lower ratings both outdoors and in domes. Brady is higher rated than Manning when playing outdoors, AND when playing in domes. Figure that one out. For me, that's the damning statement right there.
Why? Because dome QB ratings are more than 10 points higher than outdoor ratings.