Dear Aspirant, it is a good choice to pursue M.Sc in computer science after completing your BCA. It is a good choice if you mant to do masters from CS field too. The difference between MSC & MCA is that MSC is a 2 years course while MCA is 3 years course but MCA with lateral entry after doing BCA is 2 years too. The eligibility criteria for M.Sc in computer science is to pass with an aggregate of 50% in the Bachelor's degree. I am enlisting some universities for your help - 

• Symbiosis University 
• Lovely Professional University 
• Aligarh Muslim University 
• Christ University, etc.

These universities provide very good learning and extensive exposure to their students.

Hope this helps and all the best for your future endeavors.