I think the reputation of the school will really vary depending on where you are. Obviously, in New York NYCOM will be better known. However, go to Boston and you will meet far more DOs who graduated from UNECOM. Granted, I am a little biased (UNECOM class 2013!) but I do know that over the last several years UNE has matched students to The Mayo Clinic, The Lahey Clinic, Dartmouth and UMass. I think the school you pick in some way can give you an advantage on getting jobs in a specific area of the country, so if you really enjoy both schools think about where you might want to end up working. Obviously, people from schools in California get jobs in Chicago all the time but you do and can make connections based upon the area of the country that you go to school.
Good luck in making your decisions and congratulations on getting accepted!