Nitesh, It depends on what you want do do? Study a specialisation of a particular subject and be a specialist (MS) in a particular field or do a formal and broad program (MBA) involving various subjects a business manager would have to deal with.
The MS and MBA degrees have their own value and you have to decide what you want to be in future. You can do a MBA for overall knowlege benefit and then take up the MS to become a specialist. This would be excellent. Though I understand the time involved hence I have put the major differences between the two programs. You need to decide between a MS and a MBA depending upon your career choice.
All the best .