Hi 

There is no hard and fast rule about chooseing any particular institute for getting job in ISRO. ISRO do not conduct ant placement drive to hire engineers. To get job in ISRO , ISRO conducts their own entrance exam and interview. 

So according to me if you are not getting into IIT, then try for NIT then give preference to any priviate university.

Manipal Acedamy of higher Education is good , VIT is good.