If my subcontractor worked at her home in one state, but I and my business are in another state, what state do I put on her 1099?

The answer depends on where the work was performed.

If the work performed for your business was completed by the subcontractor in their own state remotely then it would be the state of the subcontractor.

However, if the subcontractor physically performed the state where your business is located then the state listed should be your state.