Pujols and Bonds have completely different things going for them. for immediate impact in terms of overall numbers, Bonds is your man. He's 38 though, which is a consideration in keeper leagues - particularly if there's no limit on how long a player can be kept.
Pujols has youth on his side, and he also plays at shallower positions and gives you some flexibility. That might change in the future, though...
It's an awfully tough call, and seems to be more a question of philosophy than player value. If it were my decision, I'd rather have Pujols.
I'd certainly at least consider several other players. Randy Johnson, for instance, would be a sweet pick at #4 if you're looking to win this year. (Check out the first round
of our non-keeper mock draft for some others to keep in mind.)
It's hard to gauge what other owners will do, but I think that under this format, Prior will go off the board very early. With his potential, I'd say that's justified, although you can probably draft a Josh Beckett, who has a similar ceiling (blisters aside), much later. Burrell and Dunn also won't last very long, even though Dunn's perceived value went down a bit last year. Phelps shouldn't go very early if he only qualifies at dh (if he's a catcher, that's a different story). Wells also shouldn't be picked too early, since there are many comparable outfielders around. Pineiro is interesting - my sense is that in many drafts, he'll be taken several rounds later than he should...
Hope this helps you plan ahead!