You should choose JNU for MA in Philosophy. It offers better learning opportunities. JNU is also the best economical choice. MA Philosophy from JNU costs only INR 654.
JNU has wonderful History, Aesthetics, and Sociology department. This is an advantage if you want your Philosophy course to be thoroughly interdisciplinary. The residential university life of JNU is a unique learning experience in itself.
One of my friends graduated from Pondicherry University and having read online reviews of the alumni here are some things you should know about them.
JNU is good in all respects. Pondicherry University is a good university, but it is nowhere near JNU or DU.