No need to make the decision now. See how the snorkeling goes. There is a big difference between the indoor skydiving and breathing underwater. Given his reaction to a leaking mask, I would be hesitant to do anything other than Pool diving in immediate contact with an instructor.
I don't know enough about your son (age and capabilities) to really answer the question, but I have taken a friend's daughter underwater in their pool and just let her breathe for a minute or so. I don't know her exact medical diagnosis, but I'll just leave it at "issues" severe enough that she will never live alone unsupervised. It did not really register with her to the point she loved it or hated it. I was directly in front of her at all times and all we had to do is stand up if there were any problems.
Would his doctor sign off on a medical release in the first place?
See how the snorkeling goes, if there is an interest, see if you can find an instructor and a pool to do a try dive the go from there. The instructor can make a recommendation as to what to do from there once he has worked with your son.
Great advice everyone! My son has Aspergers (aka high functioning autism) which means in his case high IQ, low social skills, and sensitivity to some stimuli (loud prolonged noise). Other than the zero affect when he speaks, you can't really tell he has anything. Since getting fitted for a good scuba mask, he has gained a lot of confidence. We will likely stick with snorkeling for a while until he gains confidence. We went swimming tonight again, and he was diving to the bottom and doing underwater flips again. Slow and steady will be our pace until we get as far as he can go. Then we'll have fun there.