I have always gone to Front Royal Canoe Company, they are just outside of Front Royal on Rt. 340, its around $20 per tube and they never charged me for a cooler tube. There is another one called Shenandoah River Outfitters that charges $18/tube and then another $6 for a cooler tube. I've never been tubing in Harper's Ferry but I have heard that it is a fun trip.
http://www.frontroyalcanoe.com/