I'm also of the opinion that Hendrix was not the "best" guitar player. And looking back, I don't think it was really how well he played guitar that made him so legendary. After all, his music is not that difficult to play. It was how revolutionary his music was, which was defined by his remarkable guitar work. While Clapton may be better at playing guitar, he is only doing so in the shadow of all those who layed the foundation for that type of music. Hendrix literally invented his own style and took music into an entirely different direction. And in that respect, no one will ever touch him. So it really comes down to how you define greatness. Is it how technical one can be; how catchy the melodies are; how inventive one can be? It's all subjective. You can untimately make an arguement for either one.
I think Slash is easily the most underrated guitar player ever. I say this based on the fact that (1) he is fucking awesome and (2) he was not even mentioned in Rolling Stone's top 100 guitarists of all time, which was a travesty imho. Then again they had Kurt Cobain ahead of Carlos Santana and LOL @ that.