With all apologies to the great season of Tom Brady, it's no longer a slam dunk that he's having the greatest passing season in NFL history.
Brady's mediocre day Sunday vs. Miami (79.7 passer rating) leaves him at 117.2 for the season -- a hell of a rating, but behind Peyton Manning's tremendous 2004 season (121.4). 
Does that mean that Manning's season was greater than Brady's?
The basic numbers are pretty much a dead heat:

Passer ratingTD/INT     YPAPPG
Brady 2007117.2 48/8 8.336.7
Manning 2004 121.4 49/10 9.2
But there are other points to ponder.
One factor is relativity to the league average. The league average in 2004 for passer rating was 82.8, and Manning's 121.4 was 46.6 percent above the average. Heading into Week 16, the league passer rating was 81.7, so Brady is approximately 43.5 percent above the average.
Advantage: Manning. 
Of course, Brady amassed a 15-0 record (so far) to Manning's 12-4, so that's a big edge. And the Patriots had to play their home games outdoors (in some bad weather) while Manning was indoors.
Advantages: Brady.
It's certainly debatable which season was better, and Brady's 2007 and Manning's 2004 aren't the only incredible passing seasons of the Super Bowl era.
You could make a pretty good argument for at least two other seasons as being right up there -- Joe Montana's 1989 and Dan Marino's 1984, to be specific. 
Here are the four seasons, with "% League" referring to the difference between the player's passer rating and the yearly average:

Passer ratingTD/INTYPAPPG
% > League 
Team record 
Brady 07117.2 48/8 8.336.7
Manning 04 121.4 49/10 9.2 32.6
Montana 89 112.4 26/8 9.127.6 49.214-2
 Marino 84
108.9 48/17 9.032.8 43.114-2
Is Brady's the best of all of those?
Perhaps it is -- but clearly there's room for debate. Brady's TD/INT ratio, team scoring numbers and team record are the best, but he's last in yards per attempt and in relative passer rating.
So, while Brady's season will go down as an all-time great, that doesn't mean there's no room for a little debate over whether it's THE best ever.