I was a guy in a similar situation as you -- potential to run in some D1 programs. The way I saw it, I could be an irrelevant D1 runner on a very strict regiment or a good D3 runner on a more balanced regiment. Ultimately, I went D3 and am very glad I did. Even in D3, programs are MUCH more structured, serious and organized than in high school. And there was a balance of academics and athletics that I found to be absolutely perfect.
That being said, here are some schools I think would be a good fit academically and athletically (many of which I looked at, and one of which I attend):
Grinnell (Iowa is a great state to run... and not much more)
Macalester (twin cities are dope)
St. Olaf (good program with former UMinn coach)
Kenyon (absolutely beautiful campus)
Denison (another beautiful campus, easiest to get into of these)
Carleton (academic reach but great school)
Oberlin (quirky... smart... beautiful)
Also, all of these schools have pretty sizable endowments for financial aid - if needed - isn't an issue.
Talk to coaches, get a feel for the program and visit as many as you can.