If you ask me, I would suggest you choose IIT Madras to pursue an MBA as compared to IIM Nagpur for an MBA.
If you want my honest opinion here it is. I would choose neither of the colleges you mentioned. My opinion is based on the following reasons.
But if you have no other options at all, then IIM Nagpur seems the better of the two. It is in the process of developing so maybe in some years it earns the credibility it owes to the IIM family and lives up to its name. Also some blind companies still prefer IIM students over other B Schools.