Manning is the GOAT. Championships are a team stat and the Pats would probably have one or two more if Manning had been Belichick's QB over the last 15 years because they wouldn't have lost twice the Giants. Manning 3-1 against Brady in conference title games, but that's a team stat too.
Manning is the best because he's run his own offenses and been his own de facto OC on the field, with some up and down teams and bad defenses, and pretty much owns the record books. Brady has run Belicheat's system and the advantages that have come with being in that system, both legal and otherwise.
Patriots the year Brady was out: 11-5
Colts the year Manning was out: 1-15