Hlo dear, 

I would suggest you to take CSE.

As far as I have noted that CSE students get to learn core computer science papers while IT more of general stuffs. They never had Detailed Algorithms or theory of computation which are of more importance in GATE or related exams.

Some companies specifically wanted only CSE dept students to attend the interview despite the fact that IT is quite similar to CSE. So it's better to choose CSE.

Thank you. 

• Computer science engineering (CSE) is one of the popular courses among engineering aspirants which focuses on the basic elements of computer programming and networking. Students pursuing computer science courses will gain knowledge of design, implementation and management of information system of both hardware and software.
• A student holding a degree in Information Technology can work as an IT Engineer responsible for operating computer systems, software, servers, computer networking or network securities. The programme focuses on the theoretical and technical aspects of designing, developing, researching and testing software as well as digital hardware.