Both Fenwaysouth's and my son played college baseball and received engineering degrees. The list of schools above is a good start, Cal Poly and UCDavis both have had engineering students on their rosters, plus the Ivy's, and Stanford.
We found out late in the process that STEM and D1 baseball is pretty much incompatible, except for a few cases and it almost requires that the player be a pitcher as they can come and go and get their work in independent of the team.
Unless your son is a college grad who played baseball (or you are) most people on this site do not understand how very very VERY difficult it is playing baseball and going to college with any serous major. If it is a STEM major fewer have the stamina, drive, physical and mental capacity to do it. When I got my engineering degree we lost over 50% of the students in the first year and another 20% in the Soph year. I think on my son's baseball team 2 players graduated with a STEM degree. I can honestly say that there is no way I could have maintained the schedule my son did and graduate with an engineering degree. For those whose kids are contemplating this path be prepared for them to either drop one or the other.