What should I take, IT in IEM or CSE in Heritage Institute of Technology?

In terms of college, IEM and HIT both provide similar career opportunities in the IT sector. Major recruiters like TCS, Infosys, CTS, Capgemini from the IT sector visit both the institutes. 

If you had to pick between the two engineering fields, you should always go with CS. If you select CS, you will be able to apply for a variety of government/public sector positions (ISRO, BARC, IOCL) after completing your B.tech. Only CS guys are qualified to apply for the majority of these government jobs. 

As you will get similar opportunities you can choose either. Also, outside of WB, no one cares if you're from IEM or HIT. Unless you're from JU, everything is the same.