If you are truly passionate about Physics, be it theoretical or practical, you should choose either IISER Pune or IISER Kolkata. IISER Kolkata is the best option for Physics, while IISER Pune is well-known for its overall academics and infrastructure. Here are the reasons why you should prefer IISER over IIT.

• Most students joining IIT, aim to get corporate jobs. If you are interested in the subject and want to do actual research on it, IISER is the best place. You will get to meet like-minded people too. 
• You can check the faculty and the curriculum for Physics at IIT. Even IIT Kanpur which is known for its Physics department puts more emphasis on applied Physics. Most IITs leave out theory-oriented courses like ‘Cosmology’. Also, you won’t get the lab infrastructure similar to IISER at IITs. The labs at IISERs are specifically designed for research works. From the 5th semester onwards, the course curriculum at IITs become quite different. It becomes more technology-oriented. While students at IISERs are required to do a one-year-long research project.  

Based on the performance over the last few years, IISER Pune will be better than IISER Kolkata.