Tom,
Our daughter, then 7 years old, did the pirate cruise last summer. We made the reservations about 60 days in advance, and I believe that the cruise is held only on certain days. Parents are not allowed, and I believe the cruise runs about 60-90 minutes.
Let me say-you are currently reading e-mail from one of the most paranoid mothers in the world, and I am very glad I let my daughter go. There were enough cast members along to make me feel comfortable, the children had on life jackets, and the cast members were friendly. This was one of my daughter's favorite things on our last Disney vacation.
One last thought-if the pirate cruise is booked up-there are other children's activities that Disney offers (tea parties, etc) that your children might like. Also, consider that there might be cancellations on the pirate cruise-maybe there is a waiting list).
Kathy