You should prefer top IITs then NITs for CSE branch. Apart, from them below are the top colleges for CSE

1- Birla Institute of Technology and Science

2- Delhi Technological University

3- Anna University

4- Indian Institute of Technology (Indian School of Mines), Dhanbad

5- VIT University, Vellore

6- Birla Institute of Technology, Mesra

7- College of Engineering, Pune

8- Jadavpur University

9- Thapar University

10- Veermata Jijabai Technological Institute

Good Luck!!

Here are top colleges for B.tech CSE you can prefer.

IIT Bombay- through JEE Advance
 IIT Delhi-  through JEE Advance
 IIT Kanpur- through JEE Advance

IIT KGP- through JEE Advance 

IIT Madras-through JEE Advance

NIT Trichy- through JEE Main

NIT Surathkal- through JEE Main

NIT Allahabad- through JEE main

BITs Pilani- BITSAT

Good Luck!