Has anybody tried to book a hotel in India through Expedia or any other sites? Or is it cheaper to find some agent in India.

Any experience?

From my recent experience, you should contact hotel directly. Normally they should be able to give you 30 % discount of the posted rate.
I recently stayed in various hotels in India. If the posted rate was Rs 4500/night, I was able to get the same room for Rs 3000/night. Also negotiated the Breakfast buffet in the price.