Between NLIU Bhopal and NLUJ, the latter is slightly better in terms of certain parameters. 

• NLIU Bhopal has a better reputation. It was established only 2 years before NLUJ, but it has a better alumni base. It also enjoys a locational advantage, as it is located in the same city as National Judicial Academy. 
• NLU Jodhpur has more rigorous academics and a better faculty pool.
• As per the recent NLU J placement statistics, it offers better salary packages to the students. It is also better in terms of Moot performance. In the past, students from NLUJ have won a few national moots. 

If you want to pursue Judicial Services, Civil Services, Litigation, or LLM later on then NLU J is the better choice.