Ask about the clinical education at both of the schools. Also ask students about their gross anatomy experiences/toxicity at the schools. If you are interested in a community you can get involved in, act with faculty and administrators to make changes/voice needs etc, NCNM may be a good fit for you.
Also ask the students and teachers about their faith in the medicine and how they view their practice in comparision to MD\'s and other health professions. Bastyr tends to be a bridge between MD and ND realms, NCNM tends to be less focused on this and more focused on doing what it does well. NCNM also has a little more focus on Mind-body medicine and continuing traditional, effective treatments. Hydrotherapy, homeopathy and Qi Gong are some examples of this. Both schools teach homeopathy and hydrotherapy, but there are differences in their emphysis, use and training.
You may inquire about these topics at the various schools and see where you fall as far as your comfort zone and interest...
Good luck to you-
(I attended both schools and found them to be excellent in different ways. Follow your heart.)