The OP states his child leans towards math and computer science. Do not presume your child will not thrive in a large school/classes environment if the courses are what he enjoys. Be sure that the colleges looked at offer many classes beyond the core in both subjects, as well as grad level courses. Many LACs emphasize the social sciences and humanities but do not have large course offerings in the STEM fields. Honors sequences in math can limit the numbers in a classroom. However, the lecture style format lends itself to presenting the facts and ways to problem solve which can be done for large or small groups. There are always small discussion sessions and labs for students to practice concepts and problem solving. Likewise, there are many smaller classes at large U’s for discussing literature and other fields where discussion is appropriate.
Having many professors in math and computer science departments can offer a wealth of different approaches plus many subfields of expertise. Remember- departments are a subset of larger units. Students are dealing primarily within their smaller field. Will the schools proposed offer the best education in the STEM areas of interest? Ideally you want more courses than you can take in your field available to you. Will the schools have enough courses to last four years? This is where being able to take grad level courses as an undergrad is useful. Plus being exposed to more esoteric subjects there won’t be enough students for (eg 10) in a smaller school.
Your son may surprise you with his ability to do well in a larger institution. He will get to be with students who share his interests in math et al. Much nicer having more than a few students whose other interests may not coincide. I would think he can rise to the challenges because of the benefits of the wealth of interesting classes available to him.
Short answer- look beyond your current criteria. Math/computer science lend themselves to other formats. Your son needs a lot of knowledge and skills before sitting around discussing them. He needs the benefit of many, not just a few, experts in his chosen fields.