This thread is sort of a toss up. I love Montana, grew up watching him play, saw him get the short end of the stick when Young was brought on and then he lost his job and ships out to KC.
Brady, nobody saw the guy coming. During the combine he wasn't exactly starting rumors/fires and making teams scramble for him (pun intended). You look at him now, he has probably more time in the pocket than anyone else in the league. He's as cool as can be back there. He's broken certain records and won Super Bowls.
Manning, guy plays a different game than the other two. Look at his no-huddle offense. Look at how his team hasn't won a single game without him at the helm. The team has gone through (off the top of my head) 3 QB's this year trying to replace him just to win a single game let alone save any sort of resemblance to the team pre-Manning.
Warner...I don't know if it's because I'm a Montana/Brady guy or not, but I've never like him. From Day One I just never cared for his style of play. He won two Super Bowls for two different teams that really didn't put up the numbers or play a better game than his teams, I just can't find a reason in my mind that I like the guy. I can't say for sure, but I just didn't like his game.
Best of all time, I would still go with Montana. Just based on sheer impact the guy has had on nearly every kid who watched him grow up, and he's Brady's influence too. Brady would be the successor to Cool Joe but till his career is done and the final tally is in, I'm still putting my $$$ on Montana.