Brady. Manning has all the stats, no arguement there. But who did he get those stats with? Harrison? Wayne? Edge? Clark? An incredible OLine? Pretty much. Brady had a great OLine, but not much else besides Branch, and even he isn't as good as Harrison and only arguably better than Wayne.
A QB's job is more than putting up 300 yds a game. It's more than getting 49 TDs in a season.
It's being a leader. As the quarterback, you are entrusted with the reins to the entire offense. Manning was given gold-trimmed leather reins. Brady was given threadbare pieces of cotton.
Yet who led their team more efficiently? Who didn't fold? All Manning had to do was play his cards right. Even then, instead of taking the blame himself, he would blame his line when they lost games. That is not a great QB.
Brady had to rise from being picked on the second day of the draft, rise up to being starter and command respect from every single one of his teammates. And guess what? He did it better than most can claim, and better than most will ever claim. 3 Superbowls in 4 years from dirt. As far as football goes, Brady is the true rags to riches story, figuratively speaking.
Which QB do I want to lead my team? Brady. Why? Because I want 3 Superbowls!