The Patriots haven't had a great roster since 2004. Brees wins when he has a great roster. Brady wins whatever motley collection of scrubs Belichick dredges up. Brees is coached by one of the great offensive minds in the game. Belichick is a great teacher and brilliant defensive mind, but there's nothing special or innovative about the offense he runs except Tom Brady.
If we were talking 3 championships to 2, or 2 championships to 1 or something like that, fine, I'd concede not to die on that hill. 5-1, sir. 5-1. Conference championships, 8-1.
At the end of the day, the most important QB stats are wins and championships, and that's where Brady pulls away.