Should I go for biotech at NIT Raipur and hope for a branch upgrade, or join some Northeastern NITs/IIITs? What are other options?

First of all, branch change is not as easy as it sounds and one should not take admissions solely on the pretext of changing their branches. There is intense competition, especially for the top branches and you will have to work hard to maintain a good score. 

The availability of seats depends on the number of vacancies currently in that branch. The vacancies are the least for CSE and Mechanical while the cutoffs are the maximum for these branches. 

Moreover, the college will be a new place for you so you may take some time to settle. The pressure of scoring a high CGPA right from day one might be too much of a burden. You will have to sacrifice extracurricular activities and also minimize hanging out with friends. If you think you can somehow manage and work hard you should give it a try!