To name a few of the well recognized ones (there are many others):
Harvard-MIT
Hopkins
Emory-Georgia Tech
University of Washington
Baylor-Rice
CWRU
In my opinion, BioE programs are more variable than some of the more traditional medical PhD programs across schools. By this I mean some BioE programs are very engineering-driven (device design), while others are more biologically-based (stem cell differentiation for tissue engineering). Also, at some schools/programs, the BioE department isn't under the school of medicine, so you may have other requirements and things (ie not able to cut out classes, having to TA, etc).
My suggestion would be to ask faculty at your school in BioE where are good places doing the work you are interested in, then find out from there if that school has MD/PhD and all the other intracacies.