I interviewed at both schools and I have to say I really preferred NYMC (hence why I'm going!). The curriculum is set up where you really are able to learn in a quiet environment and have the option of practicing in a huge city like NYC. You are able to choose where you go (you can even swap with other students!). With Temple and their site placements, I was really concerned about being placed in an area I didn't want, as Temple University Hospital is the most popular site and most people want it (read: super competitive). Additionally, I like the idea where, at NYMC, you can go to different places for different rotations (NYC for one, Westchester for another, CT if you want another change in pace).
The Touro merger is concerning, but it will not affect current students or the entering class of 2009 nearly as much as it may affect subsequent groups. The president issued a statement that it won't even be on our diplomas. In this economic environment, you really can't be too picky where you get your money from -- even med schools aren't exempt. I loved my experience at NYMC as an interviewee, their board scores are phenomenal and their match list equally impressive and there's even a running joke that it's called UC-Valhalla because of it's huge Cali population (I think it was almost a third of the class of 2012 if I remember correctly).
Temple was still a great place too -- the students seemed very happy and aside from the price tag, I have nothing bad to say. Bad area --> great trauma experience, right? 🙂 In the end, NYMC was my choice based on it's positives, but whatever you choose, I'm sure you'll be happy in the end.