Both are pretty good for getting you into med school but there are some differences...
The AP at CMS will, if you graduate, have you in med school next year. At BU, if you do well, you dont get accepted till a year later. Meaning you'd be looking at starting med school in the Fall of 2004. You spend that off year eitehr doing something elsewhere or doing some more coursework and research at BU. At CMS you'd be looking at entering in the Fall of 2003.
Both have you taking med courses against med students so the curriculum is somewhat similar in that sense. As for location...well BU is definitely in a more happening place. I personally think Boston is the best place to be if you're a student, so you can't beat it. North Chicago is the anti-Boston, but the city is 45 min away so it's reachable.
I could go on about the AP program, but I dont want to be redundant...it's been gone over pretty well on some other threads here so you should check it out. I can speak from experience though that it's definitely a good program and you can be successful there.