M.J.
Sounds weird, but I had success with rubbing a little breast milk in my daughter's skin. Whenever she was eating and a little dribbled out, I'd just catch it on my finger and rub it in. Worked great.
Mostly I think you just need to be patient. You baby doesn't mind the acne and it's not hurting him. I know you don't want anything to mar his perfect visage, but just leave it alone. He is still beautiful.