My applications for PhD in Neuroscience got rejected? How to be an extraordinary candidate for PhD?
You're being rejected because you're applying to top universities where the other candidates are better.  You're getting beat out on both GPA and GRE.

All but two of the schools you listed are R1 universities.  These are the top universities in the country and will be very hard to get into.  You also have a medical school, Icahn, on the list, and that also will be hard to get into, simply because it's a medical school and all of them are always deluged with applicants.  You only have one R2 university, Rockefeller, on the list.

For a top school, you pretty much have to expect that successful PhD candidates will likely have a 3.8 or better GPA and GRE scores that place them in the 80th percentile or better.  Your 3.2 UG and 3.6 master's GPA is low and your GRE scores are very low.

Consider applying to some more R2 schools or even, possibly, some R3 schools.