Over the years Prince has had baaad azzz bass players to take his bass lines and expound on them live. Can't say what the best is, far too many, but here's my take on some of the classics

Andre Cymone: do it all night/ sexy dancer
Brownmark: Head/Let's Work/Doves cry/anotherlover/dmsr/(many others)
Levi:
Sonny: space/shh/Continential/
Rhonda:dmsr/strange relationship/sign "o' times/musicology/
Josh Dunham: C. Rogers/shh/anotherlover/(from what I've seen live. Haven't seen that much yet)
Terry Lewis: The whole Time set list live/the whole Vantiy 6 set list live

Andre cymone; i'm yours.. IN THE STUDIO

I think from the 80's it would definately be Let's Work or Partyup ( I think that's Andre Cymone)

I think from the 90's probably Strollin' that walking jazz bass line by Sonny T.

I think from the 00's probably the bassline from Musicology or Chelsea Rogers

I personally LOVE the bass line on Let's Work! and it's one of my favorite Prince songs from the 80's it's SO FUNKY!