On our last cruise, we had reservations to do both of those. We would have gotten off the Cat and waited by the boats for the Disney group for the Caribbean Queen. But we left Nassau early, due to Hurricane Isabel, so we only got to do the Catamaran. It was an enjoyable ride on the Catamaran, the drinks and snack were good. We didn't go very far out in the ocean, though, and they made everyone stay in an area directly behind the Cat and only as far out as (I'm guessing) 100 yds. This was a very small space for such a large group of people. There were a lot of people getting kicked (accidentally) by other snorkelers, it was hard to move around. There is no reef out there, and no reef means no fish. Nothing to see except an old tire, until one of the crew came out with food right before it was time to leave. Then there were a lot of non-descript little gray fish.
Next time I would opt for the Caribbean Queen, although I don't know if it goes anywhere better than the Cat, there were quite a few other tour boats out where we were. My favorite Nassau excursion so far has been the Blue Lagoon Beach Day.
Hope this helps a little!