I have also heard that if you visit Atlantis in the evening, you can see the aquarium for free.
We were there on the 9-20 cruise out of JAX. We booked the excursion with Carnival, $50 each. Included the water taxi both ways, nice but brief tour of the harbor, and an awesome tour of hte aquarium. It was well worth the price just for the guided tour. The tour lasted at least two hours. After the tour we had lunch and spent the remainder of the time, until around 4:30, in the casino. I think it was worth the price to have a knowledgable tour guide.
Shirley