We did it and had a good time. We had lovely weather for it, and the ocean was very clear and blue. But I understand that if the weather isn't great, the excursion can be rather disappointing.
The "glass bottoms" are in wells, and its hard for little ones to see over the edge. My daughter was four and we had to hold her up (my five year old could see while standing). The fish aren't very clear (even with great weather) and Nassau is not exactly the Great Barrier Reef in terms of beautiful fish. It took a little longer than billed. And to get out of the reef you get a Nassau Harbor Tour - which was mostly the tour operator telling you who owned what beautiful house....the kids were board out of their minds for that twenty minutes. But the kids did think the fish were very cool, and we did see the shipwreck, which they also thought was very cool. The boat ride in itself (once we got past driving slowly by houses) was neat for little kids. We went around the backside of Paradise Island and saw a bunch of Parasailers - which was really neat for my kids.
We then went up to the Pirate Museum. The kids had a great time there, and I'd highly recommend that. Its a couple blocks worth of walking, but we had a great time.
If I had to do it again, I think I'd skip the boat tour, do the Pirate Museum in the morning, get back to the ship for lunch, put the kids in the club in the afternoon for a bit, and do a little Nassau shopping for an hour and make better use of the empty pools. We enjoyed it - thought it a little pricey but not completely unreasonable (given its basically a tourist racket) - but would have enjoyed other things more.
