You don't have to take the ship's excursion, either; it's easy to get to yourself, by taxi or water taxi. It's worth seeing once, but I personally thought it was a bit overdone. The charge to see the aquarium ("The Dig") is $25 per person. It's a matter of opinion, but I thought that was overpriced. The casino, of course, is free.
Now posting as MichelleP.
The trip to Atlantis is worth the $4 cab ride. Definitely one of Nassau's major attractions, other than the beaches. You can decide if you want to spring for admission to the aquarium and digs after previewing them in the lobby. Besides, the whole place is air conditioned.