Among NITs, NIT Trichy, NIT Warangal, and NIT Surathkal have great CSE programs. Their CSE course is at par with the top IIITs in the country.
Among IIITs, IIIT Hyderabad is the best option for a CSE course. IIIT Allahabad is pretty good too but not at the same level as IIIT Hyderabad.
Choose the institute you are getting based on your rank. In case you have the option to choose any of these NITs and IIIT Hyderabad, then compare infrastructural facilities, location, etc. to make a decision.
Not so reputed NITs like NIT Rourkela and NIT Durgapur have good CSE programs too. I received some good reviews about the CSE program at IIIT Siri City as well from my friends at the institute. But it will take time for Siri City to reach the same level as IIIT Hyderabad and IIIT Allahabad.