Baseball player deciding between Williams, Middlebury, Bowdoin, Stevens Institute

Have you considered Tufts? It is a NESCAC school though a bit different than most of the other NESCAC in what it offers including being a larger school and a University.
Tufts also has an excellent reputation overall and is very strong in STEM.
Side note, with your son’s grades and being a LHP, I would think that he should get interest from most baseball coaches at the higher academic schools. College baseball teams typically need a fair amount of pitchers/arms (long season, double headers, etc.) and there are not as many LHP as RHP.