So I talked with my first year MD/PhD friend in the lab. He was a Physics ugrad at UFL and applied looking for programs strong in imaging. Together we came up with a couple issues.
First, one has to consider whether they want to be in engineering or physics. Some programs are going to force you to do engineering if you do imaging research. We thought CWRU was probably a good example of this, though that's from a shared impression and may not be 100% true. Some programs, if they view this as engineering, may not let you do an MD/PhD with Radiology research at all as they don't take engineers (UCSF could be an example... Though, they're strong in fMRI?).
Another issue is that there aren't that many imaging MD/PhDs in general, so it's really hard to get a feel for how open a school is to having them.
Here's a small list we came up with. It's not all inclusive, but we went through schools that we knew had strong imaging cores, strong MD/PhD programs, and seemed to take a reasonable number of imaging interested people.
Penn -- Biophysics or Bioengineering. The med school in general produces a TON of Radiologists, the most in the country some years.
Stanford -- Very strong imaging group, unsure of details
Harvard
WashU
NYU -- A couple of ex-Penn people from this lab
CWRU
UMichigan -- Strong in rad-onc especially