I had the same decision to make, and I chose Nova. My reasons were that I felt that their facilities (labs and clinic) were far superior. I have friends currently in optometry school that complain about how outdated and sparse the equipment is, and I felt that Nova definitely had the upper hand there. Also, I feel like Nova is up and coming. Yes, NECOhad a long history and reputation, but so did PCO a decade ago and now I think they're on the decline. I feel like Nova, I order to compete with some of the higher profile (and larger alumni base) schools, really tries to go the extra mile. Also, their clinic really allows you to see a very diverse population. Lastly, for me, the students that I met at Nova really left more of an impression on me than those that I met at NECO.
That being said, it was a really tough decision to make. I know multiple optometrists who graduated from NECO, and none of them had a single negative thing to say about their time there. They have a bigger reputation and larger alumni base, so it may be easier to make connections (although I have no doubts that if I am successful at Nova that I will have trouble finding employment). You also get everything that a city like Boston has to offer such as history, culture, sports, great food.
Either way, I'm pretty sure you can't go wrong!