Which is a better option: an MTech in food at NIFTEM or an MS in food at CFTRI for a BE graduate?

Among NIFTEM and CFTRI, the former is a better option. It is unique and the grooming and exposure that you will get at the campus are better than any other campus that offer food technology degrees. 

For a post-graduate degree, textbook learning may not be up to the mark. But if you are industry-oriented then, it is one of the best options for you. 

For the first two semesters, you will need to study around 8-9 subjects and do two visits under Village Adoption Programme. For the third semester, you will have to do a semester-long internship. You will be evaluated based on the projects that you handle during your internship. For your final semester, you can get your internship extended, get a PPO in a company, or come back to campus and take a research project. In recent years the highest CTC offered at the institute was 8-10 LPA.