M.Sc

As the acronyms suggest MCA focuses typically on the application side whereas M.Sc. Focuses on the Science / core concepts. Hence, in general, I would recommend M.Sc. Over MCA. Having said that, there are a lot of factors that one needs to consider before making such a choice as:
Curriculum: Pay attention especially to courses covering core concepts like
Data Structures and Algorithms
Theory of Automata
Operating Systems
Programming Languages
Compilers
Technologies covered: Make sure that you weigh in the coverage of technologies from the current trend like Machine Learning, Virtualization, Python, Docker, DevOps tools like terraform, ansible etc. During the course. Hand on work: The amount of hands on work like labs, projects, practical training, internships are an important aspect to consider. Institutes offering the course: Having all the above factors the same, MCA from institute X might still fare well than M.Sc. From institute Y in some cases. It is based on factors like facilities, faculty, alumni network, joining students of an institute. You need to consider all these factors for deciding between two courses towards your career progression. Some of this analysis applies for any two courses and not just MCA versus M.Sc. Good luck for choosing the right direction for your career!