Judging thrash guitarists by solos is like judging bricklayers by the shape of the chimney. In this genre the right hand is the instrument and the lead break is decoration, so any list that ranks by lead playing alone is measuring the wrong thing.
What follows is judged on riff writing first, right hand technique second, and lead playing third, which is the order the music itself uses.
Jeff Hanneman

The best riff writer the genre produced, and the answer to this question on the criteria above. Hanneman wrote "Angel of Death", "Raining Blood", "South of Heaven" and "War Ensemble", which is four of the ten most important pieces of writing in thrash, and he did it with a vocabulary that nobody has successfully imitated in forty years.
He was also, with Kerry King, half of a lead partnership that abandoned melody entirely in favour of atonal chaos, which was a decision rather than an inability and which is a large part of what makes Slayer frightening. He died in 2013.
Marty Friedman

The best lead player, and it is not close. Friedman's phrasing draws on scales and bends that come from outside Western rock entirely, and the result is melodic without ever being predictable. Rust in Peace is the record, and everything on it that makes you stop what you are doing is him.
Dave Mustaine
The most technically demanding writer in the genre, and an underrated rhythm player. The riffs are chromatic, they move in ways that do not follow from the previous bar, and they are frequently harder to play than the solos over them.
James Hetfield
The best right hand in heavy music, and the most consequential. Hetfield's downpicking is faster, more consistent and more physically committed than anybody else's, and it is the reason a generation of guitarists learned to play that way. He is also a considerably better riff writer than his reputation as the singer allows.
Gary Holt
Exodus, and the most underrated writer in the Bay Area. Holt's riffs have no wasted bars and an internal logic that makes them satisfying to play as well as to hear, and he has been doing it since 1980. He later spent a decade filling Hanneman's place in Slayer, which is the closest thing to an official endorsement this genre offers.
Alex Skolnick
Testament, and the man who brought a harmonic vocabulary to Bay Area thrash that it did not previously have. He studied jazz, he can play things nobody else in this genre attempts, and the remarkable thing is that he uses almost none of it unless the song needs it.
Mille Petrozza and Denis D'Amour
Two writers who built their own languages. Petrozza's German vocabulary is denser and less melodic than the American one and it fed directly into death metal. D'Amour of Voivod wrote with chord shapes rock guitarists did not use, not from theory but from never having been told which ones were forbidden, and there is nothing else like it in metal.
| Player | Band | Riff writing | Right hand | Lead |
|---|---|---|---|---|
| Jeff Hanneman | Slayer | Best in the genre | Excellent | Deliberately atonal |
| James Hetfield | Metallica | Very strong | Best in metal | Rarely plays lead |
| Dave Mustaine | Megadeth | Most demanding | Excellent | Strong |
| Marty Friedman | Megadeth | Not the writer | Good | Best in the genre |
| Gary Holt | Exodus | No wasted bars | Excellent | Solid |
| Alex Skolnick | Testament | Melodic and clever | Very good | Most musical |
| Mille Petrozza | Kreator | Built a dialect | Relentless | Functional |
| Denis D'Amour | Voivod | Invented a language | Unorthodox | Unclassifiable |
What the right hand actually costs
Downpicking every note at two hundred beats per minute is a forearm endurance event, and the difference between a player who can hold it and one who cannot is instantly audible: the moment somebody starts alternate picking to survive, the attack goes uneven and the riff softens.
That is a physical entry requirement, and it is the reason the founding records sound the way they do. It also explains the injuries. Tendon problems, elbow surgery and nerve damage run through this genre, and several of the players above have had operations that a session guitarist would never need.
Who is missing
Kerry King, deliberately, because he is a rhythm player and a noise maker of genius rather than a writer of Hanneman's class, and the Slayer catalogue makes that division fairly clear. Kirk Hammett, whose lead playing is more famous than it is distinguished. Eric Peterson of Testament, who does most of the writing that Skolnick gets credited for. Jeff Waters of Annihilator, who played almost everything on Alice in Hell himself.
And the technical wing, whose best players are covered separately because comparing Watchtower's guitarist to Gary Holt is comparing two different jobs.
The other half of the engine room is in The Best Thrash Metal Drummers, and the full map of the bands is in the bands you need to know.
The gear, briefly
Less interesting than the playing and worth a paragraph, because the sound is more repeatable than people assume.
The founding tone is a Marshall or a Marshall derivative driven hard, frequently with a boost in front of it to tighten the low end, and a guitar with a humbucker in the bridge position. Hetfield used an ESP, Hanneman a Jackson, Mustaine a Jackson and later his own designs, Holt an ESP. None of it is exotic and almost all of it was chosen because it was available.
What actually produces the sound is the right hand and the palm, not the equipment. A player with the technique will sound like this genre through almost anything; a player without it will not sound like it through Hetfield's own rig. That is the single most useful thing to know if you are trying to learn any of this.
How to hear the difference between them
A ten minute exercise that teaches more than any amount of reading.
Play thirty seconds of "Raining Blood", then thirty seconds of "Holy Wars", then thirty seconds of "Bonded by Blood". Same instrument, same technique, three completely different ideas about what a riff is for: Hanneman builds tension out of one ascending figure, Mustaine crams three ideas into a bar, Holt writes the most economical thing that will do the job.
Then play something from Nothingface, and notice that the chords underneath are not chords the other three would ever have played.
Sources and notes
Judgements are editorial. Jeff Hanneman died on 2 May 2013. Writing attributions follow album credits.