Big fan of Steve Vai, VH, Satriani, etc, but I do not call them heavy metal. Hard Rock, maybe, but Vai and Satriani fit in a category outside of Hard Rock and Heavy Metal.
Malmsteen is maybe the "best" shredder I am familiar with, but that kind of music wasn't my thing. I was more into interesting licks than how fast and heavy they can sound.
I am fascinated by how Satriani was inspired to play guitar by Hendrix, and took it to a whole new level of technique and study. He's way beyond Hendrix in theory and structure, yet he still idolizes Jimi who was possibly the most influential rock guitarist ever.
It's really hard to pick a best, because there are different styles, and even different definitions of the various genres. I'm a huge Van Halen fan. I just love his sound, especially back when he was drunk and came up with so much different stuff. He was a huge influence for the Hard Rock and even Glam Rock era bands, and I know MANY people who got into playing because of him. Is he the best? No. But he had something going on that came through in his turned on so many people.
Steve Vai, I have so much respect for, and I think he may have been one of the best rock guitarists, in both theory and in playing. But there are albums of his that I have no desire to listen to. Then again, I sometimes listen to Passion and Warfare and just marvel.
There is no one right answer here, but maybe there are a few wrong answers. I mean, when the National Academy of Recording Arts and Sciences of the United States chooses Jethro Tull as the first Heavy Metal Grammy winner, you gotta wonder...