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. 

There are two aspects of an engineering degree; a corporate and a research-oriented outlook. If you are someone who wants to enter the corporate world, IIT Madras has much better opportunities. There are a number of companies that come with decent roles. The campus life at IIT Madras with personality development through activities and fests is much more suitable for those aiming for corporate life.

However, if you are targeting the research area, no institute has better facilities than IISc Bangalore. Many IITians apply every year for a summer internship at IISc. the quality of projects you will be working on combined with the top-notch faculty guidance offers a smooth pathway for higher studies at top foreign universities.

However, if you aren't sure of your area of interest yet, choose IIT Madras as it excels in both corporate lives as well as research facilities. Thus you will have many options to choose from.

 IIT Bombay is undoubtedly far better than IISc Bangalore in Microelectronics. It is important to understand that Microelectronics comprises sub-branches such as digital electronics, analog electronics, and devices/nanotechnology. Your choice of sub-branch will determine your course of study.

If you are interested in devices/nanotechnology, then one of the biggest advantages that IIT Bombay offers is infrastructure and facilities. IIT Bombay is the only institute in the country that has a clean room and advanced lab facilities, making it an ideal place to study devices and nanotechnology.

For digital electronics, IITB boasts the best possible faculty. The professors teaching digital electronics are not only respected within the institute, but they are also popular and renowned in leading industries. Thorough knowledge and understanding of the subject matter are encouraged and imparted to students.

IIT Bombay campus offers a plethora of extracurricular activities, making it an ideal choice for those who like to balance their academic and personal lives. With a diverse student body, you will find people from various backgrounds, adding to your learning and social experience. B.Tech students play a crucial role in organizing extracurricular activities, making them stand out as leaders.

One of my friends had both options, MTech in IIT Delhi and MTech in IISc Bangalore, however, despite his hailing from Delhi, he chose IISc Bangalore over IIT Delhi. Some strong reasons which influenced his decision were

• The Institute has excellent research facilities and approaches second to no other engineering Institute in India.
• IISc Bangalore does not have a BTech program and thus the entire focus of the faculty resources, education, and resources are invested in the Master's program unlike IIT Delhi, where BTech is given more importance.
• IIT Delhi has a higher intake of UG students than PG students and they are given more preferences and attention than UG students.
• Being situated in Bangalore, the IT hub of India IISC has close ties with IT companies visiting frequently for some or other events or technical competitions
• Most GATE toppers prefer IISc or IIT Bombay over IIT Delhi and so do the companies offering placements.
• The overall ambiance of campus life is more tranquil in IISc Bangalore than in IIT Delhi which is an overly populated and polluted city.
• IISc is being recognized by foreign universities and one can pursue their Ph.D. with a degree from IISc.

All these pointers strongly inclined my friend towards IISc and he eventually completed his MTech from there.

The main agenda of IISERs and NISER is to promote research culture and motivate the students to conduct extensive research as a part of their curriculum. 

My friend was a student at NISER and she loved the research environment there. She claimed the physics faculties to be extremely proficient in their respective areas of research. In fact, the Head of the Department of Physics even bagged the Shanti Swaroop Bhatnagar Prize. 

Specifically speaking, it has great scope in high energy physics and condensed matter physics. The lab facilities of the new campus are top-notch. Moreover, the UG course of the School of Physical Sciences at NISER is comprehensive and covers various areas of physics such as quantum mechanics, relativity, cosmology, etc. The best part is that you get the chance to attend 242 credit coursework in rider to fulfill your MSc integrated course.