Brady
I am not sure Manning is really intrinsically more marketable, but he certainly has people marketing him more aggressively than Brady (and is willing to do more stupid commercials than Brady is).
Endorsement agreements for Patriots seem to go primarily through the team, which is why Brady commercials usually are for Patriots corporate sponsors and also feature other Patriots members. I seem to recall hearing the standard Patriots contract says the Patriots have some control over endorsements, and that may explain a lot.
If Brady really does intend to go into politics someday -- as some have said but no idea if it's true -- he's wise to limit endorsements anyway.
By the way, I have to laugh when the only endorsement I see regularly from Big Ben is a big plastic wall hanging of himself. Such marketing power at work!