I had the same problem with skunks under the deck, a few years ago. An older guy I work told me how to get rid of them. Take a shallow dish like a pie pan. Fill it with just enough moth balls to cover the bottom of the pan. Place something absorbent like cotton balls covering the moth balls then sprink household ammonia on the absorbent material. Just enough ammonia to saturate the cotton balls but not dripping wet. Place the pan under the deck or where ever the skunks are living.
There is a chemical reaction between the ammonia and the moth balls that really puts off some fumes. My wife complained about the moth ball smell but, i asked her if she would rather have skunk smell or the moth balls. The moth ball smell does go away in a few days.
I've used this method several times and had success every time.