I got an AIR rank of 3964 in the JEE Mains. Which one should I prefer, MNNIT Allahabad for computer science or electronics or DTU for software engineering?

Both MNNIT Allahabad and DTU are well-established and much-reputed colleges. If you get admission to any of the colleges, your future will be bright and you will land up really well in companies.

Moreover, choose a branch that excites you as it is equally important as the college you will take admission in. If programming excites you, then MNNIT CSE is the best choice. If not, you can go for hardware options i.e. Electronics. Though, I'm not sure how good the software engineering of DTU is.

In terms of placements and research areas, MNNIT is not extreme but fine. You won’t get excellent faculties but you will learn a lot from their experiences. Try not to be depending on your faculty in your college life. You'll have to develop your interest and learn on your own.

Do not think only about the college but make sure you choose the correct branch as well. Both are equally important as you know that your future will depend on them.