All the three colleges are good. However, according to me, NIT JSR and BIT Mesra are better than NIT Agartala. For a core Engineering branch though, NIT JSR is a better choice over BIT Mesra. So your preference order for Civil should be NIT JSR> BIT Mesra> NIT Agartala.
Here are a few comparison points between NIT JSR and BIT Mesra to helTithi agp you choose between the two-
BIT Mesra is a better option for CSE. However, for a core branch, NIT JSR is a better choice. My brother chose Civil at NIT JSR over Civil at BIT Mesra and he did not regret his decision. Also, never choose an institution based off of NIRF rankings because they consider many factors, and many of them are irrelevant for you.