First, every person's situation is unique so one-size-fits-all advice is difficult. Your DS will be what is colloquially referred to as a "self-Prepster." IOW, he is not sponsored by USNA (as Foundation students are and which virtually guarantees them an appointment if they successfully complete plebe year).
A couple of thoughts. IMHO, prep school is best for those students (and candidates who received turndowns) who need one or more of the following: (1) maturing/seasoning; stronger academic prep (often because they went to a terrible h.s. and thus need a higher level of coursework); improved study skills. If someone is truly ready (personally and academically) for a first-rate college, he/she is better off going to college -- at least in my view.
Second, quality of prep program counts. I honestly don't know one from another -- but USNA probably does. The ones they use for Foundation are obviously highly regarded. That, however, doesn't mean there aren't other great prep schools in the country and also doesn't mean that if you self-prep at one of the Foundation schools you are more likely to receive an appointment than someone who self preps elsewhere -- provided it is a good school.
Will a PG year hurt your son? I would hope not. Some prep schools pride themselves on getting quite a few self-prepsters into SAs (however, check this statistic carefully as some include sponsored prepsters in their tallies). Every year, there are self-prep candidates who obtain appointments. However, the advice USNA gives reapplicants is to attend a civilian college/university, not a prep school.
You might have your DS contact his RD and ask about the PG school he is considering vs. a college, based on his entire packet -- which USNA has seen and I haven't. The RD can't really recommend one over the other but might say something along the lines of, "Either is perfectly fine" or "We recommended a four year college." Each of those remarks would be telling.
Finally, I suggest you consider the ultimate goal. If the goal is to attend USNA and your DS doesn't "need" a prep school, then he is probably better off at a university. If your family is considering life in general for your DS and there is a strong history of success in college/life with a prep year, then do it for that reason. And let USNA fall where it may.