IIT

It depends on what you want to pursue. For NDA, your marks don't matter much. In NDA, they can choose a person with 65% marks and can also deny a person with 95% marks. They need personality, attitude and working abilities which will suit defence forces. While talking about IIT's they are the best colleges not only in INDIA but among the top 100 of the world {some, not all}. Getting into IITs is not easy but if you get into them the lifestyle, character, image, etc. will change and I am pretty sure that a person in an IIT is also among the respected one in the society.

You have not mentioned about the rank you obtained in JAM. However, the previous year closing ranks for IITs and IISc are given below for M.Sc. Biotechnology and Integrated M.Sc Ph.D. in your category for an idea.
1. IIT Bombay : 88
2. IIT Roorkee : 227
3. IISc Bangalore (Integrated Ph.D. ): 115
4. IIT Bombay (M.Sc. Ph.D. Dual Degree): 299
5. IIT Kharagpur (Joint M.Sc. - Ph.D) : 241
6. IIT Indore: 241