Here's how I did it:
1) Go to a school's website. I used this
to find math PhD programs, but try not to put too much stock in the rankings.
2) Find the research section of the school's page. This can sometimes be hard to find.
3) Look for faculty that research what you're interested in. If you find lots at one school, apply to that school.
Ask a professor you know who researches what you're interested in. When I did this the prof I asked turned out to be fountain of helpfulness, and ended up giving a lot more advice than just schools to apply to. This is also a good way of finding out what level of school to shoot for. I would recommend doing both of these things.