We are removing a wood floor because it was wet and we needed to dry subflooring. But in removing it there is 1000's of staples in subfloor. Is there a tool to remove them without being on your hands and knees?

Hire someone else to be on their hands and knees. Only kidding. I would if you went to the extream of removing all the flooring. Remove the sub-floor as well. Cut close to the walls and reinstall new. Its a lot of work but the end results will be much better then pulling all the nails out. If the floor was nailed properly you would end up destroying a lot of the sub-floor anyway pulling the nails.
I assume you checked with your insurance company to re-emburse you for this expense anyway?