For pure science, IISc is the obvious choice among these. It is the best in India, in terms of research interface, faculties, and alumni base. 

If you are particularly interested in Physics, you should definitely choose IISc. It has an excellent Physics department. IISc Bangalore, Department of Physics has a Theoretical Cosmology group. The research interest of the group mostly involves early universe cosmology topics. For pure science courses, the preference order for these institutes is - IISc>>IISER>NISER. 

First, you should note that none of these institutes don’t offer a degree in Cosmology. Yes, all three have courses in Cosmology but these courses are extremely hard. NISER and IISER are comparable. Both are great institutes with remarkable statistics. But in the current scenario, IISc is the best option. Here are the reasons why.

• It has a better faculty base.
• Much better research environment.
• A far more established alumni base.
• It also has better recognition globally. 

If you are thinking about doing a UG course then IISc is the best option. It stands out because of the degree they deliver that is BS. It is a four-year-long course during which you can play around with your topic and narrow it down more for your BS thesis. Many alumni of IISc even co-authored research papers before their 4th year. Arnab Rai Chowdhury, Tarun Deep Saini are to name a few. IISc is best if you are certain that you want to study Cosmology. 

However, IISc is not interdisciplinary or transdisciplinary like IISERs. So, if you are not dead sure about Cosmology and need to explore to understand it well then IISER K is a better option. 

If you are considering these institutes for your Masters then IISc will be the best option. You will get to meet people from various backgrounds. The BS by research at IISc can help you get into IIA. 

Consider NISER only if you are not getting IISc, IISER-K, IISER-P, IIST B.Tech (Physical Science).