Out of the top 100 list that rolling stone provided I would say Eddie Van Halen as a combination of having the outright ability/talent/chops to play just about anything and being influential and revolutionizing how to play guitar.
I think a lot depends on when you grew up and what type of music you like. I was never that impressed by Van Halen. To me, they were always an Arena Rock band.
Clapton may not play fast and loud, but his talent is undeniable. I think he is also a musician's musician. He has played on a lot of tracks with a lot of different bands of his day without credit, including the famous Beatles Rooftop Session. His time with Cream pegs him as a founding member of the 'second stage' of rock, the first,or founding stage,being defined by the likes of Muddy Waters and Chuck Berry and Bo Diddly.
While I was reading the wrong version of the list, I came upon an introduction by the guy who started the list. When He revisited it he felt that limiting it to 100 was not fair. It should have been more like 500 and in his mind Jimi Hendrix was # 1 and everyone else, #2.
Heck, the way Neil Young plays, you gotta wonder why he made the list. He is, however, the grandfather of grunge rock and, if you have heard some of his early obscure stuff, he is also much more technically competent than his style of playing belies.
Context is another thing to consider. Look at Hendrix. When compared to guitarists that came after him, what he did does not seem all that radical, but when you look at how the electric guitar was being used when he hit the scene, he really is in a league all by himself. I would, to some extent,argue the same for Clapton when he showed up with Cream.
