I would vote for NYMC over CMS, but it is mainly for personal reasons - how I felt when I visited the schools, etc. Having now been at an entirely pass/fail school this year, I can say that it makes a huge difference!! I'm not sure how different an H/HP/P/F system is from an A-F scale, but I am glad to not have to deal with it. Find out what the passing grade is for each school and ask students (many of them) what they think are the best and worst parts of the curriculum, how competitive students are truly (for example, UCSF is thought to be ultracompetitive, but I haven't experienced it once in my class and would never characterize it in that way), what percentage of students fail an exam or class in the first two years and what happens when someone does fail an exam/class, what the social scene is like, what opportunities are out there for clinical experiences in the first couple of years, how many hours per week you are in class/lab and how much studying the average student does, etc. Basically, pick the brains of current students, ask for honest opinions (understanding that there may be a disconnect between what they value vs. what you value) and what it is like to be a student there. Like I said, from my discussions and interactions, I would have chosen NYMC - but that is a highly individualized decision. Hope this is helpful. Good luck!
-- Becky