Definitely plan a trip over to Paradise Island and tour Atlantis, its worth the time. We did a ship excersion that included a harbor tour and the tour of Atlantis and the water ferry back to the pier. Its something you should see and there is also enough time to walk around town when you get back and do some shopping. Enjoy!
Actually - my favorite shore excursion in Nassau is the Yellowbird party boat. This will be my 8th time going to Nassau and the 8th time going on this excursion - of course, do Atlantis later in the day.