Hi Kaartik! Its a bit hard to say without more details. I don't know about how the reputation of those institutions compare, but I don't know how important that is to you. A few things you can consider:
What sort of offers are you getting from each school and how do these compare with the cost of living in each city?
What sort of research will you be doing at each school? Does one interest you more?
If you have an advisor at each school, how much have you talked to either of them? Is there one who you felt you got along with better?
How do you feel about each of the cities that the schools are located in? (weather, lifestyle, etc...)
Those are just a few criteria that you can use to make a decision.