This is always such a hard question, and gets so many arguments going aswel, haha.
Personally, i don't think you can decide on a 'greatest guitarist ever' until you literally have heard EVERYONE in the world, for all we know, there could be some 11 year old virtuoso from Japan that is classicly trained and just, amazing.. but we don't know of him...
Aaaand, i don't think you could call someone the best guitarist ever unless they literally are, the BEST, at every genre of music that involves a guitar...
But anyway, some of my favs:
John Petrucci:
Such a massive knowledge of music, amazing composer, knows about what he is doing inside-out, and not just some random shredder. He writes some really amazing melodies with so much 'emotion'.. and can play a nice dose of shred with amazing clean-ness. A very influential person to me.
Mikael Akerfeldt:
Not only does he have a great voice, both clean and harsh, he is a great composer (Opeth are a marmite band, you either love them or you hate them... those who hate them haven't been open minded enough to accept them (or they just aren't right for them), those who love them see the true beauty of the music). He has so much influence from so much obscure music, which shows a true passion to 'dive' deeper into the world of music, and not to just produce the same old Metallica over and over again). He writes some of the most amazing riffs (both acoustic and heavy), and even more amazing, his melodic lines and solo's (both soft and heavy). I think he's awesome.
Jari Maenpaa:
Amazing composing talent. Amazing at his sweeps.. and he just happens to have one of the greatest voices in metal..
Devin Townsend:
Great composer, and i like the way his guitar playing isn't "speed is everything". He has an amazing background to go with it all too. And he's come up with some of the greatest vocal lines i've ever heard.
Michael Romeo:
Great guitarist, has both speed and melody. Amazing composing skills (Orchestral parts in 'The Odyssey' are just amazing).
There are more, but they're probably the main ones