IISc, IIT Bombay
IIT Hyderabad, BITS Pilani
NIT Warangal, NIT Trichy, ISI Kolkata
IIIT Delhi, IIIT Bangalore
IIT-BHU (doesn’t have a separate MTech/MS course in CSE)
IIT Gandhinagar, IIT-ISM Dhanbad
BITS Goa, BITS Hyderabad
IIT Indore, IIT Ropar, NIT Surathkal
IIT Patna, IIT Mandi
IIT Jodhpur, IIT Bhubaneshwar, NIT Rourkela, NIT Allahabad
NIT Calicut, NSIT, DTU
IIIT Allahabad, Other old NITs, Other new IITs, Jadavpur University
Other old IIITs, DAIICT, BIT Mesra, IIEST Shibpur, COE Pune
Some other renowned institutes are - CMI, IMSc and TIFR. In terms of research (especially theoretical computer science), these are on par with IITs, NITs, IIITs and BITS.
Colleges such as VIT, Manipal, Thapar, SRM, etc. can be ranked after these only (just my opinion).
I hope I haven't missed out any college which deserves to be in the top 20.
All the best to those seeking admissions in CSE branch :) Cheers!!