Even though IIT Dharwad is very new, it has certain advantages over NITK.
IIT Dharwad carries the prestigious ‘IIT’ tag which benefits it in many ways. The government allocates a separate, bigger budget for the IITs. IIT Dharwad is under the mentorship of IIT Bombay, so it receives highly experienced teachers from the IITB CSE department.
Moreover, the CSE curriculum of IIT Dharwad is the same as that of IIT Bombay. While formulating its curriculum, the authorities took suggestions from the students. This made the syllabus student friendly. IIT Dharwad has recently shifted to its permanent campus, and it offers good extracurriculars for the students.
NITK is a prestigious college with very high rankings. But even if you end up with IIT Dharwad, you can make the most of it.