First off i am partial to Heavey Metal and Hard Rock but I'm also a guitarist and in my 47 years of life I've learned that their are greats in many genre's.
a 5 way tie for 1st are :
Jose Feliciano (no one had feliciano lol,really? are you crazy people? )
Carlos Santana
Jimi Hendrix
Roy Clark
Joe Satriani-Eric Johnson (in an interview they each pointed to the other as the best guitarist they'd ever seen and they tour together)
and about a 50 way tie for 6th from Robert johnson,Johnny Lee Hooker,BB King days to Frank Marino,Robin Trower,Eric Clapton,Ted Nugent ,Alex Lifeson,Prince,chet Atkins days and on and on and on.To be fair,it is impossible to make a list smaller than 100 minimum and probably growing as I write lol
Also Eddie Van Halen created a unique sound all his own and should be in the mix near the top as well.again the task itself is an impossible one considering all the different variables involved in judging a guitarist.Lennon was a musical genius in writing and arranging but I wouldnt place him in the top 50 as a guitarist based solely on the fact that I see no evidence of him having the opportunity to showcase his talent as someone like Satriani or Feliciano to name a couple being classical guitarist by training were able to do.Dimebag displayed a masterful performane on Cemetary Gates yet Glen Tipton and KK Downing playing dual leads as the base rhythum off eachother were one of the first guitarist to ever do so with electric guitars in metal along with Thin Lizzys Scott Gorahm and Brian Robertson but Steve Gaines and Gary Rossington and Collins of Lynyrd Skynard used a three-guitar mix in songs like FreeBird etc .I saw an exhibition once where Roy Clark had like 8 different stringed instruments and went from one to the other to create a symphony of sounds by himself as if he was mozart or bethoven like.