"Best" is subjective in this case but there is an elite level that few ever reach. Here's my overly opinionated partial list in no particular order:
John McLaughin: Single most person to elevate the art of guitar in musicality and virtuosity than anyone since Charlie Christian.
Al DiMeola: The next generation after McLaughlin. If this is any measure of a guitarist, the last time I saw him I went home and practiced all night. BTW: He's at Ridgefield in CT with his electric band (rare occurrence) on 6/21 on father's day.
Robert Fripp: A true virtuoso, if not an odd fellow. Between his alternate tunings and masterful use of all sorts of effects (Frippertronics), he has skills none of us ever even imagined and a heckova composer as well
John Petrucci/Joe Satriani/Paul Gilbert/Steve Vai: Virtuoso shredders who also have a sense of melody and composition. Check out Petrucci with Liquid Tension Experiment. Think Rick Wakeman's keyboard playing is amazing? Hear Gilbert do his organ and synth parts in Roundabout on a guitar and improve on it. Vai (check out his solo in "For the Love of God") and his former teacher Satriani are often mistaken for guys who just play fast like Malmsteen with no soul to it but they are also both superb solo composers with a great degree of feel to what they do. People also put Eric Johnson on this list but he just doesn't bake my noodle personally .
Jeff Beck: Still unique and another true master. His manipulation of the Strat and feedback is unmatched. Tradition jazz (museum jazz) guys have told me that his version of Mingus' "Goodbye Pork Pie Hat" made them think that there might be something to this electric guitar thing. Between him and Jimmy Page is why I opine that Clapton was only the third best guitarist to come out of the Yardbirds.
Tony MacAlpine: Anyone clued in to the band CAB? Playing with guys like Brunel and Chambers took this metal guitarist and elevated him to virtuoso status. The amazing thing is that he plays some excellent keyboards too.
Frank Zappa: Original, innovative, maybe a bit too far out there for some but he does things technically that have not been done before or since. His son Dweezel makes a living touring doing his music. The kid can also play.
This list does go on and on. You think, well you have to mention the sound and preciseness of Brian May or Elliot Randall's solos for Steely Dan but too many more come to mind. Stevie Ray can play. Big thick strings tuned down a whole step so he can bend them, but if you bring him up, you need to mention Robin Trower especially since he had a pre-Strat career (check his solos on Piggy Pig Pig, etc). Then if you mention Trower you have to bring up the melodic genius of David Gilmour. Then you think about instead of the Strat guys, how about Gary Moore' s Les Paul blues style (check his solos as a session guy on Mo Foster's and Micheal Lee Thomas' albums for example) who makes you think of Vinny Moore only because they have the same name but can also humble many accomplished players.
Then there's Jimi. Would we all have gone out and burnt up the tubes in a Marshall head if it weren't for him? What about Leslie West who showed us how to play fat (literally) without an abundance of notes. For many, he invented the pick harmonics.
What about Steve Hackett who was the one to inspire Van Halen's tapping? Technique, melody and composition all in one. Then you have to mention Trevor Rabin and Daryl Streumer. What about Van Halen and the brown sound on its own?
Like I said, there is a lot of subjectivity so you really can't argue against the two diverse lists started here. I didn't even go into some of those classical or flamingo cats. As long as someone gets under your skin, even if it's Kurt Cobain or Mark Farner, that's all that counts.
Finally, there are people who can play at this level whose careers died in the bars or were made useless by disco (shudder). There are those records are/were rarely heard. Brilliance lost to the ages by happenstance. Maybe some of you are on this board and think that they would be on these lists if the breaks went right for them. Remember the old joke: Q -How many guitarists does it take to change a light bulb? A-100, 1 to change the bulb and 99 to say "I could have done it better than that"
Yeesh, now I have to go upstairs and practice some more, but before I go I do have to call out ucrenegade, Yankee fan for one major failure here
If Daryl Strawberry, Keith Hernandez or Matt Snell or anyone of my Mets-Jets favorites could play at all, I would add the to the list even if they were not at this level. Anyone ever hear Bernie Williams? The dude can play some himself!