You should compare these two institutes based on the performance of the branch that you are interested in. 

ISM is different from other IITs, in the sense that it is well-recognized for Mining, Geology, Petroleum, and other related branches. Other core branches like CSE, Electronics, etc. started after it got the IIT status. So, the institute will need some time to catch up with IIT BHU for these branches.

While IIT BHU has had many years to establish a brand name for these branches. It also exhibited many high packages over the years. Although the infrastructure at the institute is poor. 

So, if you are interested in branches like Mining, Petroleum, etc. then you should choose ISM. For mainstream branches, IIT BHU is better.