Since it has not been mentioned thus far in this thread, attending a Headfirst showcase after junior year is a must for a kid with baseball skills and the academic credentials with a good chance to get in to a high academic school. Since it sounds like you and your son are aiming for eastern schools, so attending one of the sessions in August in the NYC area probably makes the most sense.
My 2017 C/RHP attend the June HF session in Sacramento the Summer leading up to his senior year. Up to that point, he really had not received any interest from HAs. That showcase will present a kids test scores and GPA on the roster for the coaches in attendance. After that session, the flood gates opened up and from July through November, it was a constant flow of e-mails, campus and camp invites, and discussions of admissions chances. Mostly D3 schools like you mentioned (but many in SoCal where we are) but some outreach from the Ivy coaches at HF.
If you are not familiar with HF, there are lots of threads on this forum about it. It is costly, but from our experience, it was the best bang for a buck where you can meet and actually talk to the greatest number of coaches from HA schools. If you do that in the Summer, then you can gauge true interest by the end of the Summer and then plan your select Fall visits around application time. And as others noted here, you will know who is truly interested based on how persistent the coach is in getting your son out for a visit during school. I cannot over emphasize how important it is to take that visit during school time, watch the team in a Fall practice or inter-squad game and even spend a night on campus if offered. My son greatly benefitted from those visits--not only seeing his potential competition on the team but in seeing what life on the campus would be like.
Finally, if your son is uncommitted at the time, consider the Arizona Senior Fall Classic (Oct of Senior year) Academic Game in your plans. It is very competitive to secure a spot in the All Academic Game, but there were over 100 coaches at that event (not as personal as HF) and my son had 10-12 follow-ups in the few days after the event. He ultimately landed at a HA D2 as a result of his performance in that game.
Good luck on the journey and enjoy the process!