I would suggest you to go to the main campus and not to other campuses of Manipal.
The main campus has the best professors and the highest reputation amongst recruiters. Also has a very strong Alumini base along with a great on and off campus life. Even a branch other than CS is better than studying at Manipal Jaipur or Bangalore.
However to answer your Question MIT Bangalore is slightly newer so go for MUJ, MUJ’s director was the ex-director of the main campus and is very good, even the facilities and infrastructure are good.