Agreed. Ultimately, the ranking of the school doesn't matter but the quality of the research that you perform. All top schools have great professors where you will have the opportunity to do fantastic research. You should choose faculty that you are interested in working with and are great professors. If more of those professors are at MIT, then go there. If more of those professors are at Rockefeller, go there instead.
I would recommend OP to contact the faculty at these two schools. Have a phone call or Skype conversation with them. That will help you a lot in making your decision.