Based on the FDA Guidance for Medical Device User Fee Small Business Qualification and Certification, as a U.S. business, you should submit Form FDA 3602 for your U.S. firm. This form is the MDUFA Small Business Certification Request for a Business Headquartered in the United States.
For your Indian affiliate, you should submit a separate Form FDA 3602A, which is the MDUFA Foreign Small Business Certification Request for a Business Headquartered Outside the United States. This form includes a National Taxing Authority Certification, which serves as authentication of the gross sales and receipts for that business/affiliate.
So, to answer your question, you should follow option 2: submit Form FDA 3602 for your U.S. firm and Form FDA 3602A for your Indian affiliate company.
Note that you must include the gross receipts or sales of all your affiliates with your own gross receipts or sales when you prepare your Form FDA 3602.
Guidance sources:
FDA Guidance, Medical Device User Fee Small Business Qualification and Certification: Guidance for Industry, Food and Drug Administration Staff and Foreign Governments, II. Overview
FDA Guidance, Medical Device User Fee Small Business Qualification and Certification: Guidance for Industry, Food and Drug Administration Staff and Foreign Governments, V. Guidance for Foreign Businesses