Hi Bharat,
There are some fundamental differences between an MS in Finance and an MBA.
1. An MS in Finance is a specialized degree whereas an MBA is a general management program. This means that an MSF will make you an expert in the domain while the MBA will give you a strong foundation across business functions.
2. An MBA degree will offer you greater focus and avenues on leadership and self development than will an MSF. So, it will equip you for higher leadership roles whereas an MSF will equip you better technically.
3. The average work exp in an MBA class will be ~5 years whereas that in an MSF class will be much lower.
4. A majority of US MBA programs are 2-years long whereas MSF programs are shorter, around ~1 year.
5. You may find it easier to get information about the employment data of MBA programs than MSF programs.

6. Many top universities will offer variants of the MSF such as Master's in financial engineering, quantitative finance, financial mathematics etc. It's best to go through the curriculum and courses of each to understand the differences.
Quite a few candidates opt to first take up an MSF, work for a few years in an analyst (or equivalent) role, and later, go for an MBA. So the choice between the two really depends on what skills you want to develop, which in turn depends on what direction you want your career to take in the next few years.
MBA programs strong in Finance: Wharton, Columbia, Booth, NYU Stern, Cornell, Darden, Tuck, LBS
More about MS in Finance:
ms-finance-86/Hope this gives you some direction. Let me know if you have more questions.

Regards
Gowri
Gowri N Kishore
Admissions Coach