Both had unique playing styles that were seeped in the blues. Rory stayed closer to his blues roots to the end and focused on getting effects out of his guitar and amp. He never went into wah wah , or other special effects so popular in those days as did Jimi.
Hendrix pushed the boundaries with effects more than Rory that is for sure and he was more of a showman too ( not that Rory was not awesome on stage!!)
Both had limited vocal ability and Jimi used vocal enhancements more than Rory.
So from a guitar playing point of view Rory was my pick.
However, I don't get caught up in the best guitarist BS. Rory is just my preference even though I love Hendrix too. There are literally thousands of guitarists out there that are amazing yet they will never become famous outside of their own town. Then there are those that just have that little something else that sets them apart both Rory and Jimi did. Or they are in the right place at the right time
Rory Gallagher was a great, yet underrated guitar player who did not get anywhere near the amount of credit that he deserved. He was not as famous as Jemi Hendrix, and he may not have revolutionized guitar playing the way that Jimi Hendrix did, but he still was an incredibly skilled player.
Jimi Hendrix had performance ability. He was a person that people liked to go see. The people bought the tickets to see him. That doesn't make him the best performer. Rory Gallagher what a much better technical player. He could play more difficult things and his tones were more pure and harmonic.
Hendrix in comparison was much more of an innovator, explorer and pioneer of new musical directions. He also had copied the same black American blues men, but he wanted to take that music somewhere new. Hendrix was similarly untrained in musical theory, but he was clearly a more accomplished all-round musician being a more versatile and inventive lead guitarist AND rythym guitarist.
But the reason why he is regarded so highly by his contemporaries was not only that he also could play with great inventiveness, sensitivity, lyricism and with much 'feeling', but that he furthered greatly the sonic scope and possibility of the electric guitar in popular music with his bold and unapologetic use of feedback, white noise, loud amplification and special effects.
I think Jimi Hendrix paid Rory Gallagher the best of compliments by saying he was a superior artist, and maybe in certain respects he was, but Jimi Hendrix is possibly the best American guitarist. There are many great guitarists but few set themselves apart like Jimi Hendrix. He is truly a legend.