It depends more on the guide and the field in which you want to work.
I would suggest IISc would be a much better option. I think it is the best research institute in India. (even world rankings tell the same!) But there are cons, as it would be taking more than 5 years to complete your PhD in most of cases.
But if you want a great campus life with vibrant cultures and activities and plus a tag of IIT in your CV, obviously go for IITK. It is doing quite excellent research at present.
There could also be a placement opportunity for you in IITK after your PhD which may not be possible in IISc.
Atlast, I would suggest you to listen to your heart, look for the guide/supervisor of your PhD, rather than institution which actually does not matter at the end of the day. Your skills and achievements during PhD matters much more than that.
Do research for your potential supervisor in both the institutions, rather than the institutions itself.
**N.B.- It is not appropriate to compare these type of high profile institutions and I have no hard feelings for IITK :)
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