I'd get the 4.7 v8 it's the "newer generation" motor, more effecient, more power and more reliable.

Dodge went from:
a 5.2 to 4.7 small V8 and gained power
the 5.9(240-250hp) was replaced with the 5.7 Hemi(340-350hp)

Also, if you want performance you can get the 4.7 with a manual tranny and I think the 5.9 only comes with an automatic. I've seen a 4.7 manual out run an RT Dakota and both were basically stock. Oh, and in the Dakotas, the 5.9 was only offered in the RT model I'm pretty sure.

Also, if you're considering the V6 they did a similar motor "redo" there, 3.9 to 3.7, but i'm not sure if the 3.7 was offered in the dakota, it was first offered in the Liberty. Maybe that helps some, just figured i'd throw in my $.02!