I know we have hashed this over before, but when I searched the forum I didn't really find a comprehensive list. Also, "the best" is just catchy, this is not meant to be a competition.
For the purposes of this thread I would even use the word "clone;" not to belittle the luthier of course but rather to be very narrow in the connotation of "Martin-inspired."
IMHO, about the only thing I'd let slide would be bolt-on neck joint, since it is so doggone common lately. Also, Martin-inspired instruments do not have to be what the luthier is known for.
So, here's a list of luthiers I would use to build a fairly tightly defined Martin inspired instrument. Dred, OM, etc. I will also of course entertain smaller shops that everyone always brings up Bourgeois, Preston Thompson, Collings, Schoenberg, Santa Cruz, etc in a separate list.
Bob Altman
Matt Arcara
John Arnold
Jayson Bowerman
Bagnasco &Casati
Blazer/Henkes
Jimmy Caldwell
Julius Borges
Laurent Brondel
Lynn Dudenbostel
Jimmy Edmonds
David Eichelbaum
MJ Franks
John Greven
Ronnie Griffin
Wayne Henderson
Ken Hooper
Howard Klepper
Koe Konkoly
Nick Kukich
Per Marklund
Jim Merrill
Frankie Montuoro
Roy Noble
Leo Posch
Mario Proulx
Bruce Sexauer
John Slobod
Caleb Smith
TJ Thompson
Kim Walker
Judge Wolfe
This is not meant to be exhaustive, and please add whoever I've overlooked and I'll put them on the list!
