Brady clearly has carried bad teams. Flacco, not so much.
I think it's more useful to look at the defense they had to work with.
Brady has managed to do extremely well with a ton of very average defenses. The Pats have been the 10th best defense by points 4 times, and Brady pulled of 12, 13, 10, and 9 wins those seasons. They've been ranked in the 20s in yards allowed 7 times, and yet are all double digit win seasons. I'm sure these are slightly inflated due to the high scoring games, but it's definitely NOT a dominating defense.
Flacco, on the other hand, has had a top 3 defense 4 of seven years by both measures (one year was 10th in yards though), and top 6 another. Ironically, they won the super bowl when their defense was more average. I'm not a believer in clutch, but if it exists, Flacco is the poster child.