I've said this before in another post, but my son too had a choice between appointments at USNA, USCGA and the NROTC scholarship. It wasn't until after he visited an active duty Coast Guard unit and air station, and spoke with recent academy grads that he changed from being all in for Navy to accepting his USCGA Appointment. CGA is less than half the size of his high school, and he will be the first to say that you simply can't fly under the radar at CGA. You will know everyone in your class, and likely most from the classes above and below your class.
Congrats to your son "academyorbust2020"! He has two great choices. Only he can choose what is best for him. Just make sure he has all of the facts to make the best choice. One thing to consider.... Obviously, USNA felt that he would be better off with another year of high level math and such, thus the offer to the Foundation program. If he thinks his Calc and Chem are weak and could benefit, that may be the route to take. Many high performing high school kids find out (sometimes too late) that they didn't have the study habits or proficiency in in those tough subjects to successfully navigate freshman year and any academy. While the thought of an extra year in school may not be appealing to your son, it is something he should consider. It could set the tone for the rest of his academic career.
While we'd hate to lose a good candidate to another service academy, your son has great options to consider. I tell kids all the time to never ever consider an offer to Prep or a Foundations program as being "second best" It can be a real gift in the grand scheme of things. Sometimes the extra year of academics is HUGE!
Just food for thought.