No matter where you ask or look, no one’s going to tell you which is better, IISER or NISER because both are equally good for undergraduate studies.

To ensure learning directly about your field of interest and look for the professors working in it, the best way is to look into the research being done at the IISER and NISER. Additionally, talking to the alumni and going through the course structure will result in a more informed decision.

You will not have any students or professors with this IIT-NIT difference mindset because deep down they are well aware that the institutes have the same goals, infrastructure, and opportunities.

Also, I find it quite lame when people compare IISER and NISER claiming the former is at par with IITs while the latter is at the level of NITs just because of the first letter they share.

IISERs and NISER are reputed institutes in the field of Science. If you want to choose among these institutes, do so based on your choice of course. NISER comes under the Department of Atomic Energy (DAE) and has a wonderful Physics faculty. Among IISERs, IISER Kolkata is the best for Physics. IISER Pune is a good option if you are interested in Chemistry.IISER Mohali is pretty good at Algebraic Mathematics. 

The video below gives a comparative analysis of IISER and NISER for a better understanding

Overall, the better institute is a matter of personal preferences more than anything

Both institutes are good for research and basic sciences. There is no clear winner between these two. The major difference between the two institutes is that NISER comes under the department of atomic energy and IISER comes under the Ministry of Education. If you are getting IISER Pune, Kolkata, Mohali, go for it. Otherwise, it’s better to choose NISER.