The choice of the branch is more important than choosing the institute because it determines and shapes your career. If you are interested in working in a PSU or have an interest in Electronics, choose ECE but if you have no such inclinations choose CS, the most diverse field. There are two main differences between IIITs and NITs
Based on the placement scenario and the academics, here is the preference order I would suggest you follow while making your choice
NIT Jalandhar CSE>IIIT Jabalpur CSE>NIT Raipur CSE>NIT Kurukshetra ECE>NIT Hamirpur ECE> NIT Jamshedpur ECE
It's important to note that this preference order is not based on any official data and is based on my own opinion only.