If you are going to take an excersion in Freeport, go with the one the cruise offers. We went there on the Fantacy and then to Nassau 3 years ago and there isn't anything really to do at all in Freeport. We took a taxi to the shopping area...that was mostly closed. The video of the people who went to the Blue Lagoon had a great time and if we do that one again, we will definitely do that in Freeport. Having not taken the tour, it seemed like a waste of a stop to us.
Nassau --I agree about Atlantis...you can take a cab or water cab of there and there is no charge to go through the hotel at all and you can pay a nominal fee ($25 or something) to go through the acquarium they have there which takes a couple of hours we were told. The ship is nice and you will have a great time!
Have fun!
Scarlet
as far as the beaches, there are a few and plenty of cab drivers to take you there 