Since "Best", especially in art, means different things to different people, there's obviously a bunch of different answers here.
Some folks love "shredders", for example, while others loathe them. This is a good example, although he's not shredding too much - I've played
this clip for a couple of hours in a row a month ago and loved it, while my Jimmy/SRV/Zakk Wylde loving friend got bored immediately.
I spent some time last year researching the fastest guitarists to see if I'll get inspired to start shredding, and I found a bunch of people I've never even heard of before. So instead of mentiong the known ones, i'll mention a few that are great but a little more obscure:
Michael Angelo Batio is as fast as hell - some say THE fastest - and does some really strange things with his hands.
Jason Becker was a prodigy, not only incredibly fast but tasteful as well. That clip was taped in 1987, when he was 18!
Paul Gilbert - he's my favorite of all the fast devils, he seems to be the most versatile one and is a funny, down to earth guy.