To compare two institutes, you need to consider various factors. A few of such parameters are briefed below. 

• Placements Statistics 
• Academics
• Alumni Strength
• Cutoff Required
• Also for CSE, coding Culture

If we compare MNNIT Allahabad and VNIT Nagpur based on these parameters, MNNIT comes ahead, although marginally. 

Here is a brief overview of the CSE program offered by the two institutes.

Other than that, you can also choose a college which is closer to your hometown, if necessary. That way you can save valuable travel time and visit home during holidays.