As you are looking for the list of Top universities for M.TECH (CSE) in India, here I am sharing the same:

Berhampur University, Orissa
Central University of Punjab, Punjab
National Institute of Technology, Tamil Nadu
Chhattisgarh Swami Vivekanand Technical University, Chhattisgarh
Haldia Institute of Technology, West Bengal
P.E.S. Institute of Technology, Karnataka
Visvesaraya National Institute of Technology, Maharashtra
Calcutta Institute of Technology, West Bengal
Sree Buddha College of Engineering, Kerala
Kurukshetra University, Haryana
College of Engineering, Orissa
VIT University, Tamil Nadu, Karnataka
Mewar University, Maharashtra
Indian Institute of Technology, West Bengal
Nirma University, Gujarat
Guru Nanak Dev Engineering College, Punjab
Bharathi Vidyapeeth University, Maharashtra
East West Institute of Technology, Karnataka
Adesh Institute of Engineering & Technology, Punjab
Maharshi Dayanand University, Haryana
Institute of Engineering and Technology, Maharashtra
Oriental Institute of Science and Technology, Madhya Pradesh
Amristar College of Engineering and Technology, Punjab
Anurag Engineering College, Andhra Pradesh
National Institute of Technology, Kerala
Heritage Institute of Technology, West Bengal
National Institute of Technology, Kerala
Dr. BabaVaheb Ambedkar Technological University, Maharashtra
Indian Institute of Technology, Delhi
Indian Institute of Technology, Andhra Pradesh
Kalasalingam University, Tamil Nadu
C.V.S.R. College of Engineering, Andhra Pradesh
Aditya Engineering College, Andhra Pradesh
Ferozepur College of Engineering and Technology, Punjab
M.E.S. College of Engineering, Kerala
Central University of Bihar, Bihar
Rajasthan Technical University, Maharashtra
Indian Institute of Technology, West Bengal
Fakir Mohan University, Orissa
University of Pune, Maharashtra
Rungta College of Engineering & Technology (RCET), Chhattisgarh
National Institute of Technology, Tamil Nadu
Indian Institute of Technology, Delhi
J.I.S. College of Engineering, West Bengal
Jiwaji University, Madhya Pradesh
Devi Ahilya University, Madhya Pradesh
Advanced Institute of Technology Management, Haryana
Y.M.C.A. Institute of Engineering and Technology, Haryana
Apeejay Stya University, Haryana
Indian Institute of Technology, Andhra Pradesh
Assam Don Bosco University, Assam
Utkal University, Orissa
Alagappa University, Tamil Nadu
Rashtrasant Tukadoji Maharaj Nagpur University, Maharashtra