As background, I'll be heading to Chicago in the fall to study security issues/IR. 'Tis a long and painful process, so start early!
Stanford, Columbia, and MIT are probably the top schools for studying security. From what friends and professors in other/similar programs tell me, Stanford is more focused on modeling and statistical approaches, while a degree from MIT may be more policy-focused. Keep in mind, also, that the classes for MIT's "security studies" field are very tightly focused on specific military concerns -- operations, etc. If that is your interest, go for it, but you may want to consider IR if not. Columbia has some great people but I've heard complaints that the political science department is too closely tied to SIPA (and thus more policy-oriented than many aiming for an academic political science career might like). My Columbia information is the least reliable, though.
Princeton is reportedly planning to put a lot of money into improving their security faculty, and they generally have gobs of money to throw around for their graduate students. Would certainly be worth applying and seeing what the deal is if/when you get in.
I've been told by several pHarvard students focusing on security not to be lured by Harvard's name and funding -- their security faculty is small and, from what students there have told me, sort of marginalized.
Yale and Chicago are also good options for security studies, though I'd say Columbia and Stanford are probably slightly better (we're still talking top 5-10, probably). Yale's faculty in the area is very small and their star, Bruce Russett, will likely be retiring relatively soon, but if you're looking at nontraditional aspects of security Yale's related departments can't be beat and there are some promising young faculty coming up. Chicago and Yale both have a reputation for being more open to qualitative, area-studies type work than most of the other top political science departments, as well.