I do not think that there is much difference between these 2 colleges when it comes to masters, academically.
Make a list of pros and cons and choose the one with less cons.
Being an MITian myself, I can tell you the social life in Manipal is way better. No hassles of city life, only the good parts!!
VIT, I have heard, is not that open minded and not that much fun. But it’s just hear say. So go ahead make a list, talk to someone from VIT and get their opinion as well.