Which institute should I join for an MTech in computer science, ISI Kolkata or one of the IITs?

IITs offer better placements for MTech in Computer Science. ISI Kolkata offers fewer core Computer Science job profiles. Most opportunities offered at the institute are for M.Stat and MSQE students. But if you want a career as a Data Scientist, it will be a better choice. ISI Kolkata placements are the best in the country for analytics. However, the recruiting companies usually prefer M.Stat/MSQE students over M.Tech. 

According to the recent placement highlights M.Tech CS students of ISI usually receive a median CTC of around INR 18.6 LPA. 

In terms of research too, join ISI Kolkata, if you want to work on something related to analytics or big data, etc. If you want a traditional career path in CS, then IITs will be better.