Well, #1 would be Jake Maclay who is still with me, but also builds on his own as Hive Ukuleles. Kind of a trick question, because he's also the only protege who builds ukes unless some of my former students have gone on to make more! That said, Jake is an utterly fantastic builder.
The field opens up considerably if you're talking guitars, basses, etc., and there I'd have to put in a good word for Bill Asher who specializes in lap steels. Electric builder Scott Walker also has worked for me off and on, and he's very good. Then there are Frank Fuller and Larry Robinson from my Alembic days. Larry is, of course, one of the very best inlay artists in the world now.
One of the hardest things that I see luthiers tackle is selling their work. Some of the best craftspeople just don't have the knack or can't handle the huge cut you have to take when selling wholesale. It's a real dilemma, and it makes or breaks independent careers more surely than the issue of craftsmanship.