chazo said:
We've done nude snorkeling quite a few times. Here's what our experience as been:

The best nude snorkeling we have ever done was at Paya Bay. Now, I'm not that thrilled with the resort, but the snorkeling was really great and they had no problem with nude (during naturist weeks). The trip to Pigeon Cay was especially worth it, though on our second visit they never got around to offering that trip. The Honduras reefs tend to be much more unspoiled.

We did the Tiko Tiko cruise in St. Martin, where you can snorkel nude. The problem with St. Martin is that it has a much longer history of commercialization and tourism, so the reefs seemed much more damaged and there wasn't nearly as much fish. It was one of the weaker snorkeling trips for us.

At Hedo they will let you snorkel nude if there are no other family resort boats around. I've been snorkeling there many times and have never worn a suit, so it's common. Reefs around Negril vary from worn out to really nice. Our last trip they took us to an area that was really teaming with fish and the reef was very nice. There's also a sunken cannon and some anchors to see. The guy from the boat swam with us and offered to take pictures with our camera, and we got lots of great shots. It was a blast.