Having played both PC games I would say it's a pretty close call on these 2.
Godfather is great but has it's ups and downs. My main issue with it was that every interior seemed to look the same after a while, and the side missions were basically the same. Sort of a generic GTA. The gameplay was great though. The management part that I enjoyed at the start, wore me out after a while. But all in all good.
Scarface is more action oriented. A ton more violence. It's straightforward. The story is actually pretty decent as is the voice acting. But for the PC the control was horrid so the Wii should bea major step up. The little bonus "pimp my mansion" thing was fun as well.... but I wont give anything away.
I enjoyed Scarface just a LITTLE bit more.