I had a similar issue a week ago: I got into 2 schools, a top 10 program and a barely top 100 program. At the top 10, my PI was controlling, I wasn't gonna get to do research I wanted to do anytime soon, they didn't really train students in more 'experimental' methods, and the funding was crap. At the top 100 program, my PI wanted to foster my projects, she guaranteed a ton of supervision, I would get training in all methodologies, the lab publishes at roughly the same rate as the top 10 lab, and (surprisingly) the funding was twice that of the top 10 program. I turned the top 10 program down today and accepted the top 100 one. My reasoning is that I figured I would be the most productive in a place where I would be the most happy (fit in the best).