Hii Priyanshu 

Both university VIT AND MANIPAL are considered to be one among the best universities across the country. 

But in comparison among these both universities you should go with VIT because it is considered as one of the preferrable university of many JEE aspirants. 

VIT is having a great posture of education system by adopting FCCI for students.

Coming to the point of CSE branch both are having the great posture as well placements. But according to me fee structure for CSE branch for both of these universities will somewhat differ. According to my point of view if you are are in the zone to select one among these both I advise you to go with VIT.

All the best