I can't say who the top three are, it's like comparing athletes from different era and in different sports. I can only say who impresses me the most based on my taste and what moves me:
Guitar:
Jimmy Paige - command and judgement like no other. Look how he styled his Yardbirds and LZ stuff. You could kinda tell when he was at the edge of his command but it worked.
Neil Young - To get a sense of what he could do and appreciate his integration it only takes Down By The River. There are many more but he used it as an artist uses color. It's not only about getting attention with it, it's more about how to weave it into the overall.
Jimi Hendrix - Best command. If he didn't want it to sound like a guitar he'd figure out how to create something new, all of it effortless. But the narcissistic approach, short catalog and integration not given much thought demotes him to 3 in my book.
Honorable Mention: Chuck Berry, BB King, Duane Allman, George Harrison
Keyboard:
Joe Zawinal - It's a keyboard, right? That's a song, right?
Patrice Rushen - The most beautiful and melodic I've ever heard. Sneaky command.
Ray Charles - Was it his blindness? Pure talent? Led the league in creating music with it.
Honorable Mention: Jan Hammer, Rick Wakeman, Lonnie Smith, Booker T Jones
Sax etc.:
John Coltrane - I can't listen without stopping what I'm doing and trying to ride along.
Wayne Shorter - Yes Weather Report elevated all of them but no-one knew better how to individualize and harmonize than him.
Clarence Cleamons - Did Bruce Springsteen really meet him in an unemployment line? To me the sax is about power, tension, melody, restraint and taking those moments in the spotlight and knowing what to do.
Drums:
Could be my ear or the role I think they play but to me they're just a metronome.
Bass:
Stanley Clarke - Somebody else do a School Days. Anybody?
Jaco Pastorius - I'm drawn to the ones who can bring it out of the background and into the music which with bass is often innovative.
Paul McCartney - The songs are so iconic it can be hard to find his bass but the best job ever of enhancing the music which is job one for it.
Next thread might be offering a play list. With streaming in moments you're onto someone else's list.