Our granddaughter, then six, did the Pirates Cruise. She loved it. I think it's one of the hidden treasures (crack myself up) of Disney World. Get there around 9:00 when the marina first opens. Your son will need to pick out a life vest (the Cast Member will later check it for a proper fit) and get his Mickey bandanna with ears and his name on it. You can then take lots of good pictures of the new pirate before anyone else shows up.
You will get a receipt and a pager when you check your son in. Make sure you have both at the end of the cruise. Right at 9:25, the pirates are grouped together and each one is assigned a buddy. They are given their instructions and they board the ship (a pontoon boat with a Jolly Roger flag). At 9:30 the ship will sail. Do not be late.
At 11:30, the ship will come back and you'll see 24 very happy and singing pirates. And they are loud! Don't miss the arrival. You'll turn over the receipt and the pager and your son will return from his adventure. It's very well done and you can see the whole boarding and unboarding process. My daughter-in-law and I took a monorail tour of the resorts while the cruise was going on.
The kids get a bag lunch (Uncrustables, juice box). And they do return with treasure. It's a lot of fun and all the kids really enjoyed it.
One small note - make sure your son goes to the bathroom before the cruise. We almost forgot and having a child on a boat and on islands with a full bladder for two hours isn't a good idea.