I've spent the better part of the past 4 years visiting high performance marine shops all over the country.
Here's a few that really stand out in the North East.
North of Boston, I highly reccommend Dorr's Marine in Windham, Maine. Tim Dorr has been maintaining race boats and Poker Runners for years. His shop is immaculate and he is up to date on all Merc schools/Certs. He's built several motors for me over the years, I could not be happier with Dorr's work.
Ocean Performance in Old Saybrook CT is a top notch facility that has been in the High Performance business pushing 30 years. Very clean, modern facility. Very experienced with all Merc products.
Long Island New York has several very capable shops, Mid Coast Performance in Patchauge and MRD Perf. in Lindenhurst should be noted.
Upstate NY is home to Sterndrive Specialists, Central Square NY(North of Syracuse) Chris has been in business for years and has a great following.
Lake George (Bolton Landing) is home to Performance Marine, Jason Saris is very well known in the industry for his honesty and top quality workmanship. They also build a killer marine engine.
Chesapeake Bay has MDG Performance in Edgewater, Maryland. Dave Gavatos is one of the most honest guys in the industry and is well known in the Bay area (actually a hidden secret) for his extremely stout engine packages. Tr I've never heard of an MDG built motor ever blowing up. MDG's motors seem to last forever.
As I think of more, I'll update.
Kurt