There are many central , state , Deemed universities in India but the best universities  are: Delhi University, Delhi

Jamia Millia Islamia,

JwaharLal Nehru University,

Lovely Professional University Jalandhar 

University of Pune,

Dr.Bhim Rao Ambedkar University, Agra

Banaras Hindu University

Anna University

Christ University,

Savitribai Phule University

The Maharaj Sayaji Rao University,Jadavpur University, 

University of Hydrabad,

It would be better if you could share which particular state you are interested in as there are many colleges and universities available in India which are good to pursue M.Sc program -

Loyola College ,chennai, St. Xaviers College, Kolkata, Thanthai Hans Roever College Barathidasan University, Karunya University school of science and humanities Karunya University, Christian College Kerala University, St. Stephens College, Delhi, Presidency College, Chennai, Kurukshetra University - Kurukshetra, Haryana., Presidency College - Kolkata, West Bengal., VIT University - Vellore, Tamil Nadu.. Jamia Millia Islamia - New Delhi, Delhi, Bharati Vidyapeeths R and D Centre In Applied Chemistry Pune, Maharashtra, Research And Development Centre In Applied Chemistry Pune, Maharashtra etc.

Good Luck !!!