I have a friend who is pursuing M.tech in Electronic systems engineering at IISc and a cousin who is pursuing M.tech at IITB too. So, I seem to be in the best position to compare IIT Bombay and IISc Bangalore.
Ultimately, the final decision depends on what your prospects are and what you expect from your college life. If your main goal is to pursue full-scale research then IISc is the best place for you but if you also want to experience a great campus life and get placed then IIT Bombay will serve you better.