My son is a 2017, but otherwise sounds like an almost identical situation for him lies ahead. Will graduate as 17 year old, so he is at a bit of a disadvantage physically. Almost 6' tall but struggles to stay above 170. He is positive he wants to do mechanical engineering, so we've gone through the same search for engineering schools that have baseball programs that are not part of the elite D1s, and then expanded to D2 (where we have found few matches beyond UC-San Diego) and D3.
One site I found helpful in building the list is this one:
I am not sure how accurate their rankings are, but what is really nice is that you can sort for engineering schools by state and see how they are ranked by state and within the region and nationally. As you scroll down the lists, once you see the engineering programs number dwindling, then you know they do not really specialize with engineering.
Then you can compare engineering schools with the various lists out there for baseball programs. This one has a good list of all D1 programs:
Good luck with the search, and come back to this forum to let us know where he ends up. You are not alone in facing these issues so it helps the rest of us to learn from others experience.