There's no more point in denying it Andrew Luck is the best QB in the NFL. Wish he wasn't a Colt... but it is what it is.
While I'd probably rank Luck at #1 as well, you could make a strong case for Brady.
Luck: 26 TD, 9 INT, 3,085 yards, 100.3 Rating, 63.6% Comp%, 393 Attempts
Brady: 22 TD, 3 INT, 2,392 yards, 103.5 Rating, 64.1% Comp%, 334 Attempts
While Luck has considerably more TD and yards, he also has 59 more attempts. That is more than an entire game's worth of passing attempts.
Brady has 3 interceptions to Luck's 9.
Brady has a better Passer Rating.
Brady has slightly better completion percentage.
The interception comparison alone puts Brady right in the discussion. Also, if he had the same amount of attempts as Luck, he'd likely have at least 4 more TD, and 400 more yards to show for it. And that's being relatively generous.
Luck does has the intangibles nod though, as he is more mobile in the pocket and usually rushes for 20 or so yards per game, and has some rushing TD.
(I'm not a Pats or Brady fan btw, just making a case)