With the NFL Draft over and done with, and team’s rosters for the most part set, today we look at which of the big three QBs—Tom Brady, Peyton Manning and Drew Brees, will have the best fantasy season in 2009.

Now injuries are the one X factor, as seen last year when Tom Brady, fresh off his MVP and 50 TD season, went down in the second quarter of week one to leave fantasy owners across the land depressed that had chosen him in the top five picks of the draft.

But if all three go through the entire season and escape significant injury, who will come out on top?

Look for Drew Brees to be the top fantasy QB, followed by Brady and Manning. In that order.

Brees last year was lights out. His team stunk, but he was putting up numbers like our fed is printing money—out of control. In fact, if not for an errant pass on his last attempt of the season, he would have eclipsed Marino’s single season passing mark (5,084). He also finished with 34 TDs.

In 2009, he should be just as dangerous. Although he probably won’t hit the 5,000 yard mark,  in large part because the defense should be improved, meaning games will be closer, he should still hit around 4,200-4,500 yards and toss between 34-40 TDs.

His skill players are dangerous: Marques Colston is a year further along in his development; Reggie Bush should be more dangerous out of the backfield; Jeremy Shockey could regain his earlier form and become a solid outlet for Brees in the short game, and Robert Meachem could become a prominent deep threat which is how New Orleans envisioned him when they took him in the first round in 2007.

Tom Brady should rebound nicely as well, but due to a recovering ACL, look for Belichick to rely more heavily on the run as he’ll want to limit Brady’s exposure as much as possible. And that’s one of the reasons that the Patriots brought in Fred Taylor to complement Laurence Maroney.

But they’ve still got Randy Moss and Wes Welker, and with the addition of Joey Galloway, who’ll probably be used exclusively on the deep ball, the opportunity will once again be there for between 3,700-4,000 yards and  30-36 TDs.

The reason why he won’t come close to 50 again, is the bitter taste of karma is still firmly entrenched in Belichick’s mouth, so there will be no more throwing touchdowns when up by 40 points in the third quarter this year.

And rounding out the three, long time fantasy mainstay, Peyton Manning.

Manning is still one of the top QBs in the league, but his star power, especially from a fantasy standpoint, is diminishing. His 49TDs back in 2005 seems like eons ago, and with the drafting of RB Donald Brown in this year’s first round, to go with Joseph Addai, it appears like the Colts plan to run the ball more frequently in 2009.

And the thinking behind running the ball more is they want to keep their defense fresh and on the sidelines as much as possible.

But that’s not to say that his numbers will fall off a cliff.

Even though Marvin Harrison is gone, Reggie Wayne, Dallas Clark and Anthony Gonzalez are still there, and both backs can catch the ball out of the backfield.

So expect Manning to hit right around the 4,000-yard mark, with between 26-30 TDs.

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