[deadhead12]

More out of respect rather than actual conviction I'll throw Jimmy Page in the pot.  

 

[cjpearson]

Bob Dylan

 

[Benaiir]

Guy-Manuel de Homem-Christo

 

[batphink]

If the question was more specific (ex: who's the greatest guitarist alive) there'd be more of a debate but there's only a handful of musicians who can play multiple instruments well.
 
My #1 choice is Prince.  His songwriting is wildly uneven but there's no denying his skill.
 

 
A distant #2 is Billy Corgan.  Artistic quality dropped a bit when the original Pumpkins split up but technical quality remains high and he always puts on a good show.
 

 
#3 is Imogen Heap.  She's often compared to Kate Bush but I think she's better.
 

 
#4 David Bowie.  As a musician, he's very underrated.
 

 
#5 Dave Grohl
 

 
 
Honorable mention: Peter Gabriel.  In regards to his musical ability, he's very humble.  He prefers to have other musicians perform his songs.
 
Dishonorable mention: Trent Reznor.  Two years ago, I would've ranked him #2 but lately he's been god-awful.