morningwoo

Penelope Higgins is excellent.

Bloomington immediately springs to mind because it has Sumit Ganguly who is well-established in the field of South Asian security studies. He is only one guy but he is well connected and provides a good ecosystem for his grad students for publishing articles and jobs afterwards. I second Mocha's suggestion of Penn. Devesh Kapur heads the Center for the Advanced Study of India (CASI) and that provides a good avenue for interested grad students to engage with people in the field. Then there's Ashutosh Varshney at Brown who's known for his book on communal violence in India. From what I understand, Brown's program is more qualitative as well, if that appeals to you. Johns Hopkins SAIS might be another place to check out. It's a policy program, not an academic one but their expertise in South Asia is decent. If you want to go into a public policy career after your PhD then of course, it's best to be based in D.C. If you are interested in Security, MIT has a fairly solid program. Vipin Narang has recently taken up an Assistant Professorship there after getting his PhD from Harvard.