Hi there Melissa,
I can understand your concerns! While normal 3-D movies are great fun and very enjoyable, I'm not sure if your son is going to be overwhelmed by the ones shown at Walt Disney World.
In my honest opinion I would have a family member who is close to your son and knows him well watch the movies beforehand to make sure that he can handle the environment. While he may not get some of the effects in certain seats, There is still a lot of sensory effects all around him.
To me, the most intense movie is It's Tough To Be A Bug at Animal Kingdom. Well, that is besides Star Tours which is also a motion simulator and I'm thinking you may not want to him go on that one as well. But, unfortunately, I do not know your son personally, so I cannot say for sure what he is going to enjoy.
Definitely, when you arrive at your first park, make sure to go by Guest Services and ask them if they can provide a Guest Assistance Card. The card allows certain privileges to make your trip with your son more manageable. All you need to bring is a note from a family doctor detailing your son's sensory issues,
There are many questions and answers about the card on the Moms Panel site and if you need anything please feel free to ask! Thank you so very much and I hope you nave a wonderful trip!