Eric:
If your son is considering attending Wheaton then forget everything I said. My son would never forgive me for giving aid to the enemy
Seriously, I know Wheaton to be a great school with a strong baseball program. There is a member of the board who has a son pitching for Wheaton. Perhaps he can tell you more.
The LEC has a number of strong programs and as like2rake mentioned, ECSU is certainly one of them. They handed Babson their only loss in the past 10 games.
NE is great for D3 baseball because there are so many schools playing at a high level. You don't have to travel far and you're going to face tough competition 5 or 6 days a week. Coming from playing year round in AZ my son was concerned that his teammates might not take their baseball as seriously as he did. That has not been the case at all as his whole team works year round to get better and to prepare. It sounds like your son has earned the enviable position of having no bad choices. I'm sure he's going to have a great college baseball experience.