Both institutes are relatively new and enjoy a similar status and brand value in the education world. IIT Palakkad is a new IIT while IIT Dhanbad although an old institution has recently been given the IIT title. So that leaves us with preference as the major factor in determining which institute is the right one for you.

MNC is a blend of both Math and Computing concepts and is often very rigorous. The mathematical proofs and theorems form a major part of the curriculum and CS comprises just a minor portion of it. Unless you are a math lover or are genuinely interested in it, this branch might be very challenging for you as the concepts are very advanced and nothing like what you studied before. CSE on the other hand is an evergreen branch with broad prospects. 

Moreover, the faculty of IIT Palakkad are from IITM also thus improving the quality of education offered. The infrastructure is excellent with great accommodation facilities.