I believe you wish to compare the bachelor degrees of both institutes (based on another question you’ve asked, as this question doesn’t provide that detail), and want to know whether to proceed with a BSc in Agriculture, or a BS-MS degree from the IISER you’ve been selected for.
Unfortunately, there is no “best”, between either of them.
At least, there is no single criteria, that can unanimously declare one of the two to be the “best”.
You need to compare the coursework of both degrees, and see what best suits your interests, and assists you in developing the knowledge necessary for your career plans.
It is your degree. It is your education. It is your career choice.
Hence, it is your responsibility to do some work, and figure out what each degree offers you, and find what suits you best. Do not depend on random people over the internet telling you which one is the “best”.
Because we all have biases, and decisions about your career should not be based on someone else’s opinions.
If you’d ask me what I would pick, I’ll say a BS-MS in IISER, because I’m not interested in agriculture at all. But a different person may prefer ICAR.