John S,
RJM is spot on.
Your son starts by creating a vetted list of colleges that are a fit for him. Vetted academically and athletically by him, you, his coaches, his guidance counselor, scouts, other third parties, etc.
Once that list is compiled, he reaches out to the baseball coaches and the admissions reps of the schools on his list. Engaging the baseball coaches is always important. Engaging the Admissions reps and expressing interest is particularly important at D3 and at schools where the coaches may have less pull.
From a baseball perspective, he'll need to be seen by the coaches on his list. That's typically at college camps and showcases. For some kids it's also at travel team tournaments.
He goes to the showcases and camps where the schools on his vetted list will be this Summer. For many rising Seniors, this is the Summer that they must be seen.
Good luck!