We spent 2008-20010 in the Western Caribbean. Through the canal and east to the San Blas then west and north, up the western coast to Bocas Del Toro, up and around the turn and west to Roatan, Rio Dulce, Belize, Mexico and up to Key West.
Roatan was the best as far as underwater is concerned. Just beautiful. We spent a month in the Bay Islands of Honduras.
There is no place where tourists really take over. I wouldn't think too much about it. Most tourists that go to the Bay Islands are adventurers that are pretty good. The Bay Islands are laid back.
If you're going to the Bay Islands I'd head to 'West End' Roatan, get a mooring and spend a week or two getting your bearings and head out from there. We liked West End, Guanaja & the national park islands of Cayos Cochinos.
I's all good. Get an underwater camera.