Hello Priyanshu,

IIIT, Bhagalpur and IIIT, Manipur both are governed by IIT Guwahati. However, IIIT, Bhagalpur is new and is in a developing area. IIIT, Manipur is relatively older and according to students' personal experiences it is better than Bhagalpur. Manipur's area is developed and all kinds of students study there.

Personally, I would recommend IIIT, Manipur.