Welcome!
IMO, pick the school with the best academics, best guidence counselors, best track record of getting kids into top academic schools (ask to look at things like the "Naviance" software program which tracks that specific HS's college admissions stats), best motivating teachers, best classes which motivate students. In other words, bet on the next 50 years instead of betting on the baseball future of a middle schooler.
Individual baseball skills can be (and will be) built outside of any school program (so find great individual coaches); and the size and success of a HS baseball program or its coaches is irrelevant to any specific player's chances of being recruited/drafted. If a player is good, and the parents have an understanding of the process (recruiting and finding a good academic fit in college), a player will be found.
It's great he is good and motivated in baseball and has supportive parents. I assume the same is true on the academic side. It comes down to this (in 3 - 5 years): the better the combination of baseball skills and grades/scores the more college options are available. (Every college kid with pro potential in the country is found - regardless of location, school size, division, league. But that stage is wayyyy into the future with lots of speed bumps in between.)
If your son has issues with reading or other academic skills (e.g., study discipline) now is the time to address it.
It's great you're looking ahead - but it's the combination of baseball and academics which can really give a kid leverage in reaching for a top college - thereby keeping all options open (baseball and the next 50 years).
JMO.