Just a few things.
1). I absolutely despise the Patriots. You'll NEVER hear the words "Go Patriots" escape my mouth, unless absolutely necessary (i/e Miami needing New England to win to make the playoffs).
2). I also think in the media, and in common discussions, people tend to WAY overblow the accomplishments of individiuals or teams and float the term "GREATEST OF ALL TIME" around way too freely. Case in point, I greatly disagree with those who say the '07 Patriots have the greatest offense of all time (hell, to me they're not even the best of this DECADE) and I also feel putting Bellicheck up there with Halas, Lombardi and company is obsurd.
That being said, I disagree with several things said in this thread.
Is Tom Brady a system QB? Perhaps. He certainly benefits from having a team with a very solid offensive line and defense. However, a guy who won Super Bowls with Antwan Smith, Kevin Faulk, Troy Brown and David Patten as "targets" and put up record breaking numbers with Wes Welker as his #2 go to target and a player in Randy Moss most of us wrote off as being done (why do you think the Raiders were only able to get a 4th rounder for him?) is hardly the benefit of a system.
Since Brady took over at QB, the team has changed coordinators several times, changed supporting casts several times and yet they've continued to do one thing consistently-- win.
You take Tom Brady off the Patriots, they crumble. Maybe not crumble to the bottom of the NFL, but I'm also pretty steadfast in my belief that the Patriots wouldn't have three Super Bowl rings had Bledsoe remained at QB and I'm sure as hell is hot that they wouldn't be 17-0 with Matt Cassell at QB and the team that stands the best chance of catching the '72 Dolphins as the NFL's only unbeaten team in modern memory.
I widely admire what Joe Montana did in his career. The guy was a winner who had ice water in his veins. However, whereas he had a good Oline and defense like Brady does in New England, his offensive weapons that he had in 3 of his four Super Bowls was top notch.. He had some guy by the name of Jerry Rice as his main go to guy, he had a pretty steady handed John Taylor as his #2 Wideout and the vastly underrated Roger Craig as his halfback.
Elway, his record(s) speaks for itself, however he never won a Super Bowl until late in his career when he had a lot more to work with (i/e TD, a great OLine and a solid defense, plus two pretty good WR in Rod Smith and Ed McCaffery).
Marino? My favorite of all-time.. I've often said if he had ANYTHING in terms of a supporting cast at HB (his WRs were ok, but all of 'em were the perfect examples of players who benefitted from the QB, with maybe the exception of Keith Jackson), however at the end of the day, excuses are like.. well, you know the rest. And it pains me badly to say that.
I love those who brought up Otto Graham and Johnny Unitas. Big kudos to you, because I have both of those guys ranked up there in my top 5.. Unfortunately, in the modern era, there's a lot of people who have the mindset of "if I didn't see it, it didn't count". That said, kudos to you again for bringing them up.
At the end of the day, it's all subjective. However, you cannot (regardless of whether or not you have an opinion of him or the Patriot organization) take anything away from what Tom Brady has meant to the Patriot organization. Keep in mind, not only has Brady won games and Super Bowls there, he's also changed the overall perception of an organization. Old school fans, tell me this.. 20-25 years ago, if someone would have told you the New England Patsies would go on to be one of the all-time great dynasties, how many of you would have taken it seriously?