Definitely stay in South Beach.
What kind of hotel are you looking for? Full amenity beach front? 3, 4, 5 star? 1 or 2 blocks from the beach, but reasonable?
There are not too many boat shops close to South Beach. Cigarette is out in Hialeah. Aventura, aka North Miami has a few scattered places like Lip-Ship and TnT. Other than that, many folks are farther north like Ft. Lauderdale and Pompano Beach. OSO HQ is in Ft. Lauderdale.