guitar is such a versitile instrument and can be played in so many styles... it is hard to say who is "best" without breaking it down into genres, and even then there are millions of guys in each genre, lots of guys we never have heard of.... I mean there could be a jazz or blues guy in India who is the greatest ever but we dont hear his music.
Anyway, lately Ive been leaning towards Lenny Breau, as the greatest all-around guitarist that I have heard... his repitoire was mostly jazz but he could also play flamenco, classical, country rock etc. very well guy was a natural.
There is a difference between this type of virtuoso, and a rock guy (in most cases)... a lot of rock legends are virtuoso's with their 'sound' or their songwriting, or what they played within that genre, and their image / attitude etc....but the true virtuoso who studies his instrument for all techniques, chords, soloing, improvisation... you have to look to the jazz world for that in most cases.