Getting up and out is much harder then getting in the boat, I'd just make sure dad and uncle have the ability to lift him out.
Yes - it is not easy to get someone into the boat because the boat is so low (and fairlky tight).
It is MUCH easier to get most people in than out though.
Getting in, gravity is working for you. Getting out, you have to work against gravity in a small space where you may not have the space to use proper lifting technique.
Also, the person's ability/disability may make getting in or out harder.
A person who has low muscle tone will be dead weight, and if they don't have good head or neck control, you have to worry about supporting their head and neck in position (plus, the boat has a very low back, so you may have to support it during the whole ride).
Doing that may not be a problem for a short ride, but a long ride like Pirates will be a strain for the people doing the holding. So, make sure you are ready to lift at the end.
My youngest DD has spastic quad CP - which means her body is very stiff. When she gets excited, she also has athetoid movements, mostly of her legs.
All that means that her hips and knees don't want to bend, so it's hard to sit her down. Plus, we have the added feature of legs and arms flying all over.
Getting her in and out takes a different kind of plan than someone with low muscle tone.
The main thing is, you want to consider how his CP affects him and make a game plan for getting in and out. All boats come to a complete stop for boarding and unloading. The CM dispatching the boats does not move the boat until guests are safely in or out.
You will be getting in and out on the same side of the boat - the side shown in this picture.
So, it is a transfer to the right to get in and a transfer to the left to get out.
As was already mentioned, there is an elevator to the left of the moving exit ramp. That is hat you hold use with a wheelchair.
It's funny but everytime I've used a wheelchair at POTC the chair came into the boat with me.
A long time ago, they used to put most wheelchairs into the boat, even small ones which did not fold.
Now, in most cases, they don't put the wheelchair into the boat, even if it does fold. One reason is that the wheelchair can get jostled out of place during the ride, especially during the drop.
Another reason is that most wheelchairs are more than 30 pounds and the awkward position for the CM putting it in and lifting it out can lead to back injuries, especially if they have to do it repetitively during the day.
So, first choice is to transfer to a WDW park wheelchair. Those are available at the entrance to the queue and also at the exit. Parking your own wheelchair and using one of the attraction wheelchairs means they only have to get A wheelchair to the exit in time for the guest to get off.
That is a lot easier than getting that particular guest's own wheelchair down one floor and into another building to be there in time for that guest to exit.