I've said this before and I'll say it again.
The way to judge a guitarist: ingenuity, sound (how good and how unique), speed, and delivery. I therefore nominate Trey Anastasio (Phish). Does anyone else in the world sound like Trey? No. No one can imitate the sound that comes out of his guitar--the only other person who I can really think of who is similar on that level is Jimi--and listen to "Weekapauge Groove" (preferrably live) to hear what I am talking about. Trey's innovativeness in writing is quite well exemplified in many songs but one to take a look at are "Guyute" and "You Enjoy Myself". As for speed and delivery, "RUN LIKE AN ANTELOPE" (in my opinion, the jam in that song is the epitome of jamming). Also, for a little bit of all the great elements, especially sound and delivery, a wonderful song to listen to is a live version of "Divided Sky". In addition, keep in mind that virtually none of Trey's solos are in one key, that he can somehow hear the seemingly random notes his bassist and pianist (Mike and Page, respectively) are playing while simultaneously playing perfect correlating notes. It's quite impressive. Finally, I'm not saying Trey is THE greatest, just one of them.
Also take a look at Tim Reynolds(acoustic masterman)--not just for what he does with Dave Matthews but on his own "Turn it Into Love," "Kundalini Bonfire," "You are My Sanity," and "Stream."
Al Schnier and Chuck Garvey (Moe.) also have amazing talent. Try listening to Meat (a great version is from their L live album). to see their talent (as well as their bassist's).
Jake Cinninger and Brendan Bayliss (Umphrey's Mcgee) are constantly improving wonderments of the guitar. Listen to "Nothin Too Fancy" by Umphrey's McGee to see.