I know exactly what you're thinking because I was there, and so was everyone else that came before me that gave me the advice I'll give. Which is pretty simple and unprofound -- you're in college for the education, first and foremost. Sure, there are experiences to be had outside of the classroom that can influence your decision, including athletics, but the education is what you're after. Pick the better school academically. Even guys that went all-in on athletics and do fairly well on the collegiate level most likely have to get a "real" job out of college. Doesn't mean they have to give up the dream, just means the priority has to shift.
You can still train and run at the D1 school. There may be a club team that you can join. The social life is probably much better. The academics are better. The price of not participating in the NCAA is small to me compared to joining a meh D3 team and being unchallenged academically and ending up with a degree that holds less weight.
You want to bet on the things that are going to have the most impact on your future. Your athletic participation in the NCAA will have a smaller impact on your life than pursuing a solid degree.