Your parenthetical is almost certainly false.
I think Boston might actually have more biotech companies than NYC. Labs require space and the real estate is way cheaper in Boston. https://www.bostonglobe.com/business/2017/01/13/mass-and-rivalry-has-extended-biotech/bwfS36IRUxSq9dnfX6nITP/story.html
From an “academic preparation for medical school” standpoint, there will be no demonstrable difference between MIT and Columbia. It’s going to come down to NYC vs. Boston, Core or not, and other soft factors that separate the two.