Where can you do Mormons and JWs? I went through last year and was accepted at a number of programs with these exact interests. (Well Mormons/Seventh Day Adventists.) I think the opposite is true - rather than these being obscure topics now, they are too popular. Most of the big programs have PhD students working in these areas. I think you've left out a number of important programs Notre Dame (Marsden,) Vanderbilt, UCSB, FSU, Washington, Chicago, Indiana, and if you are doing Mormonism specifically then Utah State and Claremont would be excellent for Masters programs (not PhD.) I think the key to study new religions is to bring it into conversation with the broader ARH scene - if we aren't doing this in the statement of purpose, we probably won't have a shot.
On a side note, Harvard has Leigh Schmidt now who hardly works on just mainstream religions.
