Here are some suggestions-
1. Gunj - active in very rural and remote areas
2. Akshaya Patra - currently involved in feeding the poorest of the poor
3. Ramakrishna Mission - Religious organization but honest as hell in serving those in need
4. Red Volunteers - They are volunteers from the Communist Party doing amazing work, as is covered in media and seen by me, but they don't have a centralized payments system
5. CM funds of some states are tranparent, but I would stay away. States like West Bengal, Tamil Nadu, Kerala, and Odisha come to mind.
I would suggest Ramakrishna Misiion and Akshaya Patra as I have seen their work first hand. And you would find it easy to donate to them.