I am an undergraduate at JHU, and I work in a chemical biology lab on the Homewood campus. So here's what I can tell you about the program here:
The chemical biology research here is pretty fantastic, easily our best division of chemistry. The above posters are correct; it's very easy to collaborate with the med school as needed. One caveat: people in the chemical biology program tend to take a long time to graduate. One of the groups (I won't say which) had a 12th-year graduate student finally get his PhD last year. In my group, we just had our 7th-year graduate and we have a 6th-year and 5th-year who aren't even close to finishing up yet. So you do good research here, but it can be a lengthy process. It probably depends on who you work for and how efficient you are as a researcher. I'd be curious to know which faculty here you are leaning towards.
Also, although Baltimore is definitely more of a city than Ithaca or U-C, it's no sprawling metropolis and some the area around the campus is quite downtrodden and crime-ridden. But if you know where to go and when, Baltimore is a pretty cool place to be for your PhD studies.
Hope this helps.