Stingray swim in Nassau is not bad but not as good as Grand Caymen. If it is the same one we did, they have them penned in near the shore and you can swim around with them. Not nearly as nice as standing on the dune and having them swimming free.
Atlantis is nice but I felt like an unwanted visitor there. Pricey for a hotel tour. I would reccommend renting a jeep or scooter and finding a nice stretch of beach. Perhaps a chartering a boat.