As you are from Maharashtra, the best option for you is IIT Bombay. It is one of the three IITs which offer Biotech courses. Other than this there are no class 1 option for this kind of course in Maharashtra. 

IIT Madras and IIT Kanpur also offers courses in Biotechnology.

Some best institutes for genetic engineering in India are:

SRM University [B.Tech, M.Tech and PhD in Genetic Engineering]

Bharath University, Chennai [M.Tech in Genetic Engineering]

Aryabhatta Knowledge University, Patna [B.Tech and MTech in Genetic Engineering]

Hope it helps.