Tom Brady is in the middle of the greatest season any quarterback has ever had, and this is not even disputable. He has completed 74% of his passes (off the top of my head, I can think of only three QBs who ever completed 70% in a season: Ken Anderson, Steve Young, and Sammy Baugh). Brady is averaging 305.9 passing yards per game--short of pace for Dan Marino's record 5,084, but still a stunning number. And he has an absolutely Super Tecmo Bowl like TD to INT ratio of 38 to 4. He'll likely shatter Peyton Manning's TD record of 49, and he might do it with 6 or 7 interceptions.
Combined with Peyton Manning's relative "struggles" this season, Brady's season may lead some, like Bill Simmons, to assume "the 'Brady vs. Manning' argument was settled over these past 11 weeks" (which Simmons throws in flippantly rather than seriously, I'm sure part of his continuing effort to annoy people outside of Boston).
But while all credit is due to Tom Brady for the greatest QB season ever, guess what?
Peyton Manning is better.
Let's set aside subjective discussion involving the impact of teammates on Mannings' and Brady's performances. Let's also set aside team success (since both have had it, though Brady much moreso in the playoffs). Let's just look at stats. Brady may be having a greater individual season than anybody has ever had, but Manning has slapped together multiple individual seasons that put just about every other quarterback to shame.
For his career, Manning still edges Brady in completion percentage (63.9% to 63.1%) and yards per attempt (7.7 to 7.1) And while Brady is having a better single season than Manning has ever had (though his 9.1 yards per attempt are still just behind Manning's 9.2 in 2004), it's absurd to claim that one spectacular season somehow negates the numerous superior seasons Manning has had.
Before this season, Brady's best single-season completion percentage was 63.9% in 2001. Manning topped that (significantly) five times, in 2002 (66.3), 2003 (67.0), 2004 (67.6), 2005 (67.3), and 2006 (65.0). Brady's 2007 season may blow Manning's best out of the water, but Manning has put together many more spectacular seasons than Brady has.
Tom Brady is likely to break Manning's TD record, but before this season, Brady's career high for TD passes was 28. Manning topped that four times.
Before this season, the most yards in a season Brady ever had was 4,110 in 2005. Manning topped that seven times.
Statistically, Tom Brady's 2007 season is going to go down as the absolute best ever. But do you really think one spectacular season makes one QB better than another QB? Look at the career Manning has had. More than a single season, and more than cumulative numbers, I respect players that are able to put together several outstanding seasons (which is why Brett Favre's eight seasons with 30+ TD passes is more impressive to me than his 433 total TD passes). Manning has never had fewer than 26 TD passes in a season. He's having his ninth season with 62% passing, and he's had five seasons with 65% passing. He's thrown over 4,100 yards seven times. Manning has compiled a long string of spectacular statistical seasons.
I think we're lucky: I believe Manning and Brady are among the five to ten best quarterbacks ever to play the game, and we get to watch them compete against each other. But while Brady is probably a top-five quarterback of all-time, Manning is a top-one quarterback of all-time.