On our last cruise we were in Nassau until midnight. We booked a room at Comfort Suites for $300 and it included 4 wristbands for access to the waterpark slides, pools and dig sites at Atlantis. It took us about an hour to get off the ship, taxi to Comfort Suites (for check-in), and walk to Atlantis Royal Towers to get the wristbands. We had fun at the waterpark, and I think it was worth what we paid for it. Our kids (DS 8 and DD 11) were the perfect ages. There were a few mega slides and several tube rivers. The beach was nice, but not as good as others we have visited. Overall, it was VERY spread out with lots of meandering pathways. I don't think we will go to Atlantis again, but it was fun to do once. I think the Disney waterparks are almost as good and Schlitterbahn here in Texas is much better.
Regardless, I certainly wouldn't try to go on your schedule. If the boat leaves at 2, all aboard will be 1pm. I would need to leave by noon at the latest just to have time to comfortably make it back to the ship. That is a lot of money to pay for a half day of fun. IF this is your only port, I would find a beach, schedule a shorter tour, or find something to do closer to the port. IF this is a 7 night cruise, Nassau is not my favorite port and I would recommend just staying oboard and enjoying a relaxing day on a half-empty ship!