This is a very subjective science of course. How do you determine what "good," "great," or "best" is? But here are my personal criteria for assessing a guitarist's talent: A)Technical skill; B)Timing and tone; C)Emotional feel. And personally I value timing and tone, and emotional feel, more than technical skill.
Anyway, judging by these criteria, Carlos Santana is at the top of my list. He went poppy with "Supernatural" and subsequent releases (although his guitar work on those is still excellent), but dig deep into his older stuff and you will see a real genius. His ability to milk a single note and wrench every bit of emotion from it is unparallelled. Technically brilliant and yet always so smooth.
After Santana I would put reggae guitarists Earnest Ranglin and Junior Marvin up there. Earnest Ranglin is a brilliant reggae instrumentalist with a very Jazzy feel. And Junior Marvin played with Bob Marley for many years. Just listen to his guitar solo on "Waiting In Vain;" it's a perfect example of a great guitarist making somthing difficult sound very simple. True reggae guitarists know how to groove and always exude that subtle mystical feel.
I keep waiting for Carlos Santana to make an instrumental reggae CD! I bet that with his emotional feel and his love for good percussions he could make a great reggae record.
I play guitar, so this is fun!