There are several options for exploring Atlantis. They vary greatly with pricing depending on what level of access to the resort is included.
If you only want to walk around Atlantis to see the property with limited aquarium views, or go in the casino the entrance cost is $0 as Penny noted.
Atlantis does offer a tour for cruise ship visitors. The details can be found here.
This doesn't give access to the water park though.
The only way (to my knowledge) to get a pass for the water park area is to book a room or a nearby hotel they have partnered with that includes it as LHP mentioned. Or, buy a ship excursion that includes it.
is a link to the excursions Carnival offers for Nassau.