A couple of questions. Does the hand flapping interfere with his activities? Is it done a times of anxiety?
Often a more socially acceptable anxiety reducing activty is taught to replace the hand flapping. Your sons hand flapping is satisfying a need, so you can’t stop it, again teaching an alternative is best. In the home the best is to carry on the activity you wish to teach and ignore the hand flapping, otherwise you are spending you whole time trying to get him to stop the hand flapping.