This is one question which every GATE topper or top 100–150 rankers go through.
I myself was in great dilemma to decide which one of these. Fortunately I ended up going to the right institute which was right for me but I don’t say IISc is good or IIT Bombay is better. Both institutes provide different experiences.
I got an AIR 60 and made my mind that I’ll go to IIT Bombay and stopped checking application status from IISc. But somewhere deep inside my heart there was still this doubt if I should choose IISc Bangalore.
In the hindsight if I recall, my reasons for choosing IIT Bombay were merely cosmetic. It was “IIT” tag which was pushing me more than anything else. And that is not a good reason to choose any serious thing in life.
As they say, when you look for someone for marriage, you just don’t look how they look but how is the compatibility, how’s person nature etc etc.