In reading your comparisons I’d say you’re leaning Penn.
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Both campuses are in urban environments. The areas around UChicago seem to be a bit worse but you need to be aware of your surroundings in either locale. Penn has purchased and built housing all around the perimeter of the campus and they have on campus graduate housing as well so the area right around the school is in good shape. That being said, neither is Ann Arbor and walking alone after midnight is not a good idea at either school.
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Your concern about Wharton is unfounded. It seems like Wharton overshadows the rest of Penn because most people who post or talk about Penn are trying to gain acceptance to the business school.
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Penn seems more in line with your academic interests:
Penn: great academic offerings in what I’m interested in (compbio and CS). I’ll be double majoring in computational biology and computer science at Penn
vs
Chicago: I don’t love the CS curriculum here. They teach it in a really weird theory-heavy approach. Also not a lot of compbio / ML courses.
Congratulations on all your amazing choices!