Note that I went to a "top med school" on the east coast and am at neither of these programs for residency... thus I have no vested interest in talking one up over the other. My opinion is based on co-residents, old classmates, and residency program director opinion (at my old med school).
U Chicago >> Northwestern (they are still both great programs)
1. U of C is much more respected on a national level. Historically has better success consistently placing their students in "top" residency programs. However if you want to stay in the mid-west for residency, both are equal
2. Research at U of C trumps NW
3. NW in a much nicer looking location, though it's also a "touristy area" which is pretty bland at night in terms of social scene
4. These days, my impression is that NW is attracting better rounded students. The criteria for admission to U of C have changed drastically in recent years, becoming more numbers heavy (Wash U style) which influences class composition (and dynamic).
To summarize, U of Chicago likely better for career, Northwestern likely more fun for medical school.