We went to Nassau years ago. It is still pretty nasty. Our snorkeling excursion was cancelled. We were ported there two nights instead of one. We were not happy about that.
We booked through the cruise ship because we had heard that Freeport wasn't an ideal place to go when you are on your own.
The trip was through Reef Tours and we were very pleased with it. The snorkeling was phenomenal. We also liked K-Ron and Terry who were funny and made it even more fun. Highly recommend it.