Master of Computer Application (MCA) and Master of Science in Information Technology (MSc IT) both have one of the best career opportunities that can be choosen after B.tech or B.Sc. For both of the courses eligibility criteria and admission process is similar almost. The differences are MCA graduates have an edge over MSc graduates as the curriculum of MCA includes management modules also. If you are from IT background MSc in IT would be a great career option as it helps in getting a job in the IT sector in a well established post. MCA prepares the students for the industry job requirements so that they can do well in the corporate IT sector. In term of job scope both of these two have greater importance. Now choosing between these completely depends on your choice and ability.

Hope it would be helpful.