Obviously 'best' is meaningless. Favorites? These are not in order except Frank Zappa - he is my all-time favorite, I think.
Frank Zappa: blazed new trails, technically excellent, SOUNDS LIKE NO ONE ELSE (this last part is important to me, more important BY FAR than mere technical proficiency - which by itself is really over-rated, once you grow up enough to get past the 'wow' factor). His guitar solo on Inca Roads on the One Size Fits All album is still the greatest rock guitar solo I've ever heard: expressive, thoughtful, creative, traverses an emotional landscape, does not start in 5th gear like so many annoying 'stunt' guitarists, but does reach a lovely crescendo.
Django Reinhardt: Incredible technically (all the more so when you know his whole story), his playing always cheers me up.
Ike Turner - perhaps the most under-rated blues guitarist in history. he may have been a prick, but he sure could pick (and hit that whammy bar) - check out Ike & Tinia's version of I Smell Trouble, recorded live in Africa, off the Atlantic Blues Collection, guitar volume
Johhny Marr - Sounds like no one else...
Julian Bream - so, so, so much better than Segovia, who we nicknamed 'the perfect robot'.
Kim Thayil - another seriously underrated guitarist. His solo on 'Just Like Suicide' is magic.
John Lee Hooker - you'd be hard-pressed to find a less 'technical' guitarist, but he felt every damn note!
Clarence Gatemouth Brown - his best, most relaxed work artfully fuses jazz, Blues and Western Swing.
Jimi Hendrix (SO MUCH BETTER once he got the Band Of Gypsy's rhythm section together, but almost always incredible).
Curtis Mayfield (the man Jimi got all of his Little Wing type chord voicings from).
Robin Trower
Pete Townshend - just for the exuberance of it all!
Albert King (the man SRV copped 95% of his licks from)
Jonny Greenwood - his symphonic approach to guitar and arranging is without peer.
The Edge - love him or hate him (I loved him until U2 became a terrible caricature of itself - starting somewhere in the 90's) - he's unique
How about a least Favorite, most over-rated list?
Mine starts with: Vai, Satch, Malmsteen, Buckethead etc. - all 'stunt guitarists': technically utterly incredible and without peer, musically pathetic: their music is totally in service to their technique, rather than the other way around.
Technique is not music! Playing fast is not the mark of a great musician! Creating unique, emtionally complex (and sometimes, at least, emotionally nuanced) music and sounding uniquely like yourself and not other is the mark of a great musician.