On Nassau, I would highly recommend taking the ship's excursion to Blue Lagoon Island. They ferry you to an island just north of Paradise Island. It's incredible! A beautiful sheltered lagoon to swim in, things for sale, tropical drinks at a bar ($6 for a delicious Piņa Colada), hair braiding, swimming, snorkeling, hammocks, picnic tables, basketball, clean restrooms, showers, hiking, calypso music. Only drawback was the lunch prices - they were charging $8.50 for a hot dog or hamburger and $11.50 for barbecued ribs or chicken. We skipped lunch because of that. But other than that, we loved it. If you want to snorkel, they offer a swim with stingrays excursion along with it.
I don't know how long your ship will be in Nassau, but yes, you can take a ship's excursion to see it, but it's also very easy (and cheaper!) to see on your own. I was on the Fascination and we were docked overnight in Nassau. The Blue Lagoon excursion lasted from 9:00 a.m. to 2:00 p.m. (or 4:00 p.m. depending on when you chose to return), so there was plenty of time in the afternoon and evening to go see Atlantis. To do it on your own, just walk off the ship and there will be people trying to get you into a taxi. The fare is $4 per person. We asked the taxi driver to meet us at the hotel at a certain time for the return journey, and he did.