MCA

MCA (Master of Computer Applications) is a three-year Professional Master Degree program in Computer Science. The objective behind MCA is to equip students with the latest technologies, tools and applications in IT and to meet the ever-growing requirement of IT professionals.
A Master of Science in Information Technology (abbreviated M.Sc. IT, M.Sc IT or MSIT) is a type of postgraduate academic master's degree usually offered in a University's College of Business and in the recent years in integrated Information Science & Technology colleges. The MSIT degree is designed for those managing information technology, especially the information systems development process. The MSIT degree is functionally equivalent to a Master of Information Systems Management, which is one of several specialized master's degree programs recognized by the Association to Advance Collegiate Schools of Business (AACSB).
Main Difference b/w these two :
MCA : which is having more practical than M.Sc (IT)
M.Sc (IT) has been designed to provide necessary theoretical as well as practical training to the students in the field of Information Technology enabling them to augment the much needed skilled manpower in this area.
M.Sc (IT) basically it will focus mainly on theory , you will get practical also but not as much as MCA , so if you want to go in research field then go for M.Sc (IT) without any hick , but if you planned to go in Technical(Software) field then better go for MCA, it will give you more chance than M.Sc (IT).