Manipal VIT RVCE are all decent colleges and make it to the top 50 engineering colleges in India. Half the NITs are worse than these colleges even if you are talking of the same course. eg: Srinagar Patna Agartala Raipur Silchar Hamirpur Jalandhar Jamshedpur Durgapur

NITs Raurkela KKR Nagpur etc definitely are overall a little better particularly because of the NIT label but it isn't that they are a different league. They all fall in a similar league except top NITs Bhopal and onwards.

Any college upto top 50 is decent and doing CS IT or ECE there is not a bad choice. In fact it would be better to go for CS here than Civil in top 30 or so.