If you were to somehow find some people who were familiar with football as a sport but not with Brady or Manning in particular and laid out the evidence for each, I'd bet a paycheck that the overwhelming majority would point to Brady as the historically better QB.
However, fans can't avoid the bias. Announcers/analysts like and respect Brady, but they
love Manning. For example, he gets effusive praise for things like winning a few games with a few different no-name receivers this year (not counting the future HOF-er, of course
), when Brady has done it, apparently unnoticed, for his entire career. Manning came off a minor knee surgery, played like ass for half a season, and wins MVP. Brady comes off major knee surgery, has his second-best year (with numbers that surpassed Manning's MVP campaign), and everyone thinks he underperformed.
Conversely, any facts that could be used to diminish his image in any way (the dome advantage, for example, or the awful playoff numbers) are never addressed. He never gets called out for throwing blame around. Brady gets killed for "choking" in the SB when the last time he touched the ball with a real chance to do anything, he put them ahead...Manning throws the sealing pick-6 in the SB, and people fall all over themselves to blame the receiver.
Manning does a zillion commercials and is down to Earth, Brady marries a supermodel, still avoids the spotlight as much as possible, and is "too Hollywood" (even to a lot of dummy Pats fans).
Manning gets superhero nicknames like "Captain America" from guys with mancrushes ("The Sheriff?" Really, Jon?). Brady's still seen as a system QB by a disturbing number of people.
He's that guy some of us know who's made of Teflon. He's very good at his job most of the time, but no matter how he screws up, nothing sticks to him. Everyone else thinks he can do no wrong, and you keep wondering why. Tomlinson's another one.
That's just the way it is.
Personally, I would never want him over Brady. Ever. Especially when it gets cold.