When you say Navy, are you referring to the Naval Academy or a different commissioning source? I think the academy does treat midshipmen that wish to attend flight training, but if you go through OCS or ROTC, I'm pretty sure that if you need the surgery that you have to get it done on your own time and dime before you take a flight physical.
I would think the CG academy would also pay for PRK, but keep in mind that the majority of each CG academy class goes afloat on their first assignment. I think only around 10% of each class goes directly to flight school. I'm sure you would find more Naval Academy grads headed to flight school as their first assignment than you would Coast Guard Academy cadets. Not saying its necessarily harder to get into flight school through the CG, but with your son's situation, he may want to look at both.