A friend of mine faced a similar dilemma when he was torn between choosing IIM Ahmedabad (MBA) and Stanford (MS). He went for IIM Ahmedabad in the end. He considered the following factors before making this decision:
Geographical factors: If you want to stay in India then MBA from IIM Ahmedabad is the best choice. But if you are certain you want to settle abroad, MS from Stanford is a good choice.
Nature of career: Comparing the nature of both the courses, we find that MBA is a general one while MS is specific. MBA is related to business and management while MS is technical. Based on your interests and aspirations one can easily make a choice between the two.
If you are still unable to decide then know that you can pursue MBA in the US even after MS. The latter will offer you more opportunities.