I think a few things are being lost here. Firstly, up until this year Brady was viewed as a fantastic clutch player, but not necessarily a "QB's QB". Reggie Miller was also a fantastic clutch player, but that does not mean he was better than Michael Jordan.
Secondly, the Patriots have won 3 Super Bowls, not Tom Brady. The old "too much credit when they win, and too much blame when they lose" adage applies here. Last time I checked, Tom Brady plays one position on one side of the ball.
Thirdly, Manning still owns Brady as it pertains to records. As it stands, although Brady's 2007 broke Manning's single-season TD record, many other records Manning set that year still stand (including highest passer rating, most consecutive games with at least 2 and 4 TDs respectively) . He is also on pace to break every major statistic for a QB. Completions, passes, yards, TDs, and he already holds the 2nd highest passer rating for a career and most games with a perfect passer rating. Despite his fantastic year, Manning is still a better statistical QB. As I said, the Patriots and not Tom Brady beat Indy so many times.
Fourthly, I am not quick to anoint anybody the 'best' just yet. I am sick of hearing "the next Gretzky" or "the next Jordan" only to see players like Lindros, Daigle, Kwame Brown, and their ilk fizzle and drop. Now, T.Brady is already approaching unparalleled success, so I am not insinuating he is hack (obviously) just that a more tempered response is necessary.