Neil Young - Guitarist

I recall Dylan remarking that the strength of Neil's playing is his intuitive sense of melody.  Interpret those wild distorted solos as simple melodies and it all makes sense.        

Don't take those Rolling Stone rankings seriously.  Neil Young is a fine musician, but he's only a great guitarist in the sense that Mick Jagger or James Brown are great vocalists.

While I do like Neil Young's music I don't see anyone, especially Rolling Stone, ranking him in even the top 100 guitarists. There are many artists that accompany their singing with a guitar and many do it very well. Like Jackson Browne, Willie Nelson, and others.
But, the original post asked the question about Young's skill as a guitarist. Best 100 guitarists??? That's a broad question. You would have to include those who just play the instrument in a band or in a recording studio. The most praised musicians are those who sing, write songs, and even those who play decent guitar. Rolling Stone has a narrow focus on the true sphere of music.
There are too many names I can list here but there are ones that, in addition of singing, are excellent guitar players. Here's just a few........
Leo Kottke, David Bromberg, Steve Goodman, Glen Campbell, Vince Gill, Brad Paisley, Al Collins, Dickey Betts, and many more.
No rap on Neil Young but, as a guitarist myself, when I listen to or buy music the first thing I tune into is how the guitar sounds if there is one in the particular song.
 

Neil is a great musician, top 100 guitarist of all time is a stretch is a very good guitarist 
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A top 100 Musician absolutely.   Jeff Beck which I have seen and have a signed magazine.
Probably the most complex UNDER RATED guitarist alive ,but does it so effortless.
He lost a lot of support when he took years off in the 80s  just to get his head straight .he was playing in several great bands since the 60s.

His playing works well within the context of his music but I never considered him a great player. Huge fan though his opinions grate on me at times.