I gave this some serious thought a few weeks ago before deciding on Adrian Peterson, all day,

. The injuries to both players are significant and for the life of me, I can't figure why Manning chooses to play after a neck injury, but he's having a great year.
The deciding factor (for me) was the impact of each player's individual contribution to their team. Manning has returned to his old form and is leading the Broncos to another Division Championship. Peterson breathed life into a sputtering Vikings offense. Without Manning, the Broncos are still probably a .500 team. Peterson is the Vikings offense, without him, they return to the basement of the NFC North.
I can also see them spreading the awards around ... Peterson getting MVP of the league, Peyton getting Comeback Player of the Year, or if vice versa if Manning would win a SuperBowl. They both deserve to have their accomplishments recognized.
Of course, you'll have to make room for Calvin in there somewhere when he breaks Jerry Rice's record,

.