Depends on what you want to do. In terms of prestige, etc., probably the top lab in the country is Langer's at MIT (chemical engineering, btw).
For BME specific programs, the top two that stand out are JHU and Duke. UIUC is probably the top engineering school in the country, and they have a med school, but I am not sure about their BME program. Georgia Tech's program is outstanding, and while they obviously don't have a med school, Emory does, and there is a lot of collaboration between the two. Most of the California schools boast outstanding BME programs. UCSD is probably their best. Also, check into some of the larger public schools. Lots of money and top researchers usually correlate well into top programs (UWisc, UT, for example).
Hope this helps some.