Sorry I missed your question - I've been busy, and just saw it!
The Pirates & Pals boats have a great deal of room on both sides at the end of the boat where you board for wheelchairs &
ECVs. The closest seating will be the row directly in front of the wheelchair/
ECV spots on either side of the aisle. If I remember right, it is one step down down into the main seating area. The standard seating on these boats are bench-style seats with backs. (In cold weather, they give everyone clean, white blankets to bundle up in!)
If he can sit at a normal-height table in his chair or stroller, then I think he will be able to see over the side rail. Otherwise, you may want to plan on sitting him on one of the benches, or possibly on your lap.
He is going to LOVE the boat! There's singing, and trivia games, and the Pirate usually tries to make sure that all of the little nuggets get a prize of some kind! And, of course, beforehand there are treats galore, and a photo op with a certain well-known Pirate and his pal...

This, along with Hoop-Dee-Doo is on our "must do" list for every trip.

I hope it becomes a family favorite for you too!