I really doubt the weather is all that different between philadelphia/chicago/new haven but I'd love to be proven wrong. They're all cold (for me anything under 30 in the winter is cold, YMMV). You're going to have to put on a bunch of winter junk, it will be uncomfortable, you'll survive.
If the Yale system appeals to you I'd strongly consider Yale...but I think Penn is also kind of close to NYC so I'm not sure how much of an advantage that is for Yale, but both have that over chicago for sure.
If I were going into academic medicine I would go with the cheapest option though. At the top places people paradoxically make less, especially considering the cost of living is quite high. Harvard knows it can afford to pay people less so it does. If you're making 150k, and with taxes that's like ~100k (with state too). Live off 50k (which isn't a ton of money in an urban setting which is where you likely will end up), gives you 50k left. Now consider interest of these loans after 8-10 years of compounding at 7% while you do residency/fellowship. it's ~440k if you borrow 250k total, and 260k if you borrow 150k total. Interest wise you're looking at 30,800 and 18,375 dollars respectively.
So in one case you have 19k to pay off your debt in ~15-20 years and in the other case you have 32k to pay off your debt in ~7.
You also want to start saving for retirement at some point or a college fund etc.
If you're interested in surgery/most specialties (clinical not academic) you can see how both debt loads are very manageable, but in academia it's a real struggle sometimes.
Don't assume Yale or Penn will be more expensive than pritzker, but if they are I'd choose the cheaper option (only if you're exclusively considering academic medicine).
I also recommend reading a few articles on
http://whitecoatinvestor.com/ for better perspective. As an ex. you can refinance your loans if you have sufficient income post-residency and save a good chunk of change, but that isn't really applicable to academic medicine as the debt to salary ratio is often too high. There are still some great tips pertinent to you though.
No, medicine is not about the money, but doctors are notoriously bad financial planners and the difference between those who plan and those who don't is immense (doubly so if you're dealing with a reduced salary).
Finally
I want to reiterate that you shouldn't assume Yale and Penn will be more expensive, I just want to make sure you are informed about the realities of the financial decision you face, instead of just throwing up your hands like a lot of premeds do and say "wow lots of debt, who cares if it's 150k or 300k!" when it REALLY does matter if you're going into academic medicine. Very few doctors also have the patience to live off 50k a year for 7-15 years, if you aren't as frugal it only magnifies the situation.