Following are the good colleges for M.Sc chemistry in South India excluding IITs & NIITs

1.Loyola College, Chennai
2.Stella Maris College, Chennai
3.PSG College of Arts and Science - PSGCAS
4.Nadar Mahajana Sangam S. Vellaichamy         Nadar College
5.Srinivasan College of Arts and Science
6.MCC - Madras Christian College

You can choose any one out of these college to pursue Msc. Kindly visit their official site and check the fee structure & other facilities and decide which one is the best for you. I would recommend you to contact the alumni of these colleges to get best review of these colleges.

#Tamil Nadu

Madras University

Madurai Kamaraj University

Anna University

VIT Vellore

#Karnataka

IISc Bangalore

Bengaluru Central University

MS Ramaiah University

VTU, Bangalore

CHRIST University

#Telanagana/Andhra Pradesh

University of Hyderabad

Osmania University

JNTU, Andhra University

Sri Venkateshwara University

Hope that Helps.