Depending on the subject you have to choose the best for MSc. I am naming the popular ones here:

• IIT's(Admission through IIT-JAM)
• NIT's (Admission through IIT-JAM)
• JNU
• DU
• Central Universities
• Jadavpur University
• BHU

Also there are other universities for MSc but this are the best.

I hope this answer helps. All the very best for your future endeavors!