I'm currently in a similar situation, so I have just decided to apply to a couple top schools as well as a couple lower-down as back-ups. If you haven't already found this site, here's an easy interactive way to compare programs: http://www.phds.org/rankings/neuroscience
Also, not sure if you are limiting options based on cities you want to live in, but UNC Chapel Hill has a pretty good program and so does Oregon Health and Science University.