Manipal is not better than any of the NITs.
I say this with the utmost conviction. Even if you get a new NIT which is relatively unknown, you should rather choose that instead of Manipal. The key reason for this is simply return on investment. NIT is a low risk proposition. The fees is very low compared to the like of Manipal and even if you don't get a job during campus recruitment, you're very likely to get one off campus.
At Manipal, you will most likely get an IT placement with a menial package. The ROI is this case will be significantly less. In my opinion, you should never choose a private college for a government college unless the private college in question is BITS Pilani or Jadavpur University. All government colleges are a better long term option than private colleges.