Renee - you can walk around limited areas of Atlantis for free. IF you want to see the aquarium/dig- which i highly recommend it will cost about $25.00 per person. You enter Atlantis thru the casino, there will be a kiosk where you buy your tickets to the dig. There is a common area where you can view part of the aquarium, but you do miss out on a lot.
The beach at Atlantis is not free. You can purchase a day pass for use of the beach only- waterslides are not included.
St. Thomas - hit the beaches, do some snorkeling, do some shopping, walk to Paradise Point from the pier and take the tramway up the mountain for an amazing view of the harbor. check out this link-
www.vinow.com - very helpful
St. Maarten - beach, snorkel, shop. Grab a cab and take an island tour with a beach stop. Golden Eagle Catamaran sail is a great excursion if you want to swim, snorkel and beach.
Check out what the cruise line is offering for shore excursions, some excursions you can only get thru the cruise line.