A lot of interesting choices. Two of the popular picks I feel are terribly overrated, but I will leave that for another day.
You cannot say someone is the best of all time due to so many genres. Also playing loud and fast while acting like you are squeezing a watermelon out your butt does not mean you are great or even good.
Some of my choices:
Brian May
Carlos Santana
George Benson - especially his 1960's recordings on Verve
Paco de Lucia - one of the finest flamenco guitarists
Al DiMeola
Roy Clark - master of the guitar, banjo and fiddle
Glen Campbell - a musicians musician. There are always stories about bands asking other musicians to play on their recordings. One of the great stories of him is he would be in a recording studio working and he would ask bands if he could play with them. This was during the time when the musicians knew who he was, not when he was unknown.
Others to consider:
Sister Rosetta Tharpe - listen to her recording of "Didn't it Rain" which she first recorded in 1947/48. You can see where Chuck Berry, Duane Eddy, Carl Perkins and many others got their style.
Mother Maybelle Carter - mother in law of Johnny Cash. Known for her two finger style of playing. Picking the bass strings with her thumb while fingering the other strings.
Django Reinhardt - a Gypsy/Romani and probably the first European jazz star.
Peter Green - check out 'Hypnotized' by Fleetwood Mac
Steve Howe - rarely mentioned in this category, but a lot of his work on the early Yes albums is quite complex.
Alan Holdsworth - King Crimson and UK
Brian Setzer - re-popularized rockabilly with Stray Cats and his own band
Larry Carlton
Bonnie Raitt - mistress of the glass/bottle slide
Nancy Wilson
Robert Fripp - King Crimson. Ignoring the fact that he is a bit of a richardhead. I saw him perform a private Frippertronics show in NYC in 1981.
Jennifer Batten - mostly known as a sidewoman. Lead guitar Michael Jackson's Bad tour
Steve Cropper - Booker T and the MG's, Blues Brothers and hundreds of top 10 songs and albums. Stax session guitarist who also co-wrote "Knock on Wood", "In the Midnight Hour" "Soul Man" and "(Sittin' on) the Dock of the Bay".
Link Wray - the original grunge guitar player.
Johnny Ramone - most people dismiss punk guitar as 3 chords fast and loud. A lot of it was, but listen to the Ramones covers of songs like "California Sun", "Surfin' Bird" "Come on Let's Go" (w/Paley Bros) and "Little Bit of Soul"
Rick Derringer - I think he gets no respect. He has been performing for over 48 years. Starting with the McCoys to Edgar and Johnny Winter, Derringer and solo. He also played on quite a few other bands albums - Steely Dan ("Rikki Don't Lose That Number" is about him), Air Supply ("Making Love Out of Nothing at All" his favorite guitar solo), Bonnie Tyler ("Total Eclipse of the Heart"), Barbra Streisand, Todd Rundgren and Meatloaf. I also heard he played on at least one of the songs on "Kiss Alive II". Along with his rock albums he has also recorded blues and Christian albums.
I have been fortunate to have met a number of them (Santana, Benson, Cropper, Carlton, DiMeola, Howe, Holdsworth, Batten, Wray, Ramone and Derringer) and photographed many in concert as well (May, DiMeola, Howe, Holdsworth, Batten, Wray, Ramone and Derringer). I was fortunate enough to photograph Link Wray's last and only U.S. show of the year on October 14, 2000 at Clark University, Worcester, Mass. Most of the 70 or so people in attendance could have been his grandchildren and probably did not know who he was. He signed my rock book and I got his guitar pick after that show.
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