So here's what you and your son need to talk about. Does he want to go to a school with _______ programs and play baseball or does he want to go to specific schools and try to play baseball there as well. There's a difference.
D2s and D3s aren't stupid. They know your kid wants to play D1, which is why their recruiting timeline is later than the timeline of a D1. That being said, if your son does not have any interest from D1s at the end of June next summer, it isn't going to happen. And I mean serious interest where they're asking for grades and having you fill out FA calcs. After that focus on D2s and D3s.
There are D2s and D3s that try to poach potential D1 guys early. If it's a good fit and it works financially go for it, but don't just jump on offers because it's the only offer. I would suggest doing that 10 months from now, but not this second. So feel it out. The reason I mention talking with your son is because D3s, when they aren't trying to poach the fringe D1 guys, typically recruit from end of July to October of senior year. So unless there are specific D3s in mind that he'd be targeting specifically for their academic programs, don't worry about the D3s showing high interest. Of course they are.
As far as his options. Patriots and Ivys will recruit into August of next summer. They also have no money to give, or in the case of the Patriot League virtually no money. As far as D2s I know of maybe four or five that would be considered high academic. That means two things. It means that it may not be what your son is looking for OR it may mean that your son can get a ton of academic money. And then when it comes to D3s I wouldn't even focus on the baseball. I would let academics and financing college drive my decision making and if he's in between a few I would let the baseball determine where I ended up, but that's just me. I would never walk into an expensive mediocre school just to be able to play baseball for a few more years