I agree with Anirudh's reply! Well put.
Would just like to stress what Anirudh has already mentioned; that the primary difference between JNU (SSS) and IGIDR is the course content. IGIDR
being good for econometrics and being more mathematical, while JNU focusing more on the
development side.
So, it is up to you to decide your interest area and then choose accordingly.
Having said that, if you're unsure about your choice and want to explore options, I'd suggest IGIDR, for all the reasons Anirudh mentioned below.
@Anirudh: Hey! Where would you be planning to join?