J.,
My daughter is PDD-NOS and SPD (sensory processing disorder). She does not hand flap at all. This is often a sign of autism.
I am assuming you are getting services through early intervention. If you are in PA, these will transition to your local intermediate unit at the age of 3. The IU only provides services that will improve your child's functioning in school. They will only address the SPD as a corollary to their primary function.
If you are in PA, you qualify for services provided by private therapists and paid for by your private insurance and the state. You will need to apply for medical assistance in order to get the services. My daughter receives speech therapy, OT from Children's Hospital in Pgh, wraparound services, social skills programming, and therapy. The IU provides speech, developmental, and OT but they are really just side therapies to her main therapies. It can take months or years of therapy 1 or 2 times a week for an hour to see an improvement in SPD. If you are getting a half hour a week, you need more.
My daughter really has shown improvement after about nine months of all of this therapy. She is not "cured" nor will her problems go away with time. While your son may learn to cope, it doesn't mean he has to. He can get the therapy he needs and move toward living a productive life.
Best of luck to you.