When I am healthiest, I do replace my PEP mask therapy for actual exercise. Personally, I cough more and cough more mucus out than I do just sitting on my ass and doing chest therapy. When I am not feeling well, I do my therapy and exercise. Obviously, I still do my other nebulized treatments. I also feel like running or jogging is better for sanity sakes. haha You can go somewhere nice and walk, jog, run, bike, etc and enjoy yourself rather than sit at home for a few hours everyday.
I find it somewhat interesting that you said you feel like the vest isn't doing much for your son. I live in Canada and they've done a couple studies showing that the vest is not as efficient as other forms of therapy such as the PEP mask, etc. and there were 10 times more exacerbations with people using the vest. Maybe ask your doctor is there are other forms of chest physio that he could do to see if it works better for him!