There are various good and esteemed colleges in India where you can pursue Masters in Zoology. Some of them are listed below. Starting from Central top universities.

1. JNU
2. Banaras Hindu University
3. Hyderabad University
4. IISc Bangalore
5. St Stephens College Delhi
6. Miranda Hose College Delhi
7. Hansraj College Delhi
8. Ramjas College Delhi
9. Visva Bharti University Bolpur
10. St Xavier College Mumbai and Kolkata
11. Presidency College Chennai And Kolkata
12. Sri Venkateshwar College Delhi
13. Gargi College Delhi
14. Jadavpur University
15. Indian Institute of Technology
16. National Institute of Technology
17. Maulana Azad College Kolkata
18. IISER
19. NISER

Hope this helps.