IISc Bangalore is more than 110 years old and it is the first choice of most students for Science, Engineering, and Technology-related courses. Seven IISER were established recently with the goal of providing quality education in pure science. IISERs were established with the expectations that they would reach global standards in the field of basic sciences and offer intensive research like IISc.
IISERs offer courses such as BS-MS, integrated Ph.D., and Ph.D. to students. Although IISERs were established recently, they have good faculties and research facilities. Getting admission at IISc is more challenging compared to IISERs.
Among IISc and IISER, the former is the better option.
However, the research culture at IISER is quite good. If you have the option to join IISc, you should go for it, otherwise, IISER is also a good option.