JimmyB,
I've seen wide-ranging amounts from 5-20% per weekly/charter net rate. But to answer your question - typically charter cost, not the total cost+expenses. What I found online...
"At the conclusion of the charter, it's customary for guests to leave the crew a gratuity of between five and 15 percent of the charter fee, based on your satisfaction with the service rendered. Good crews will not make it obvious how hard they're working to take care of your every need, but they do work very hard, often from sunrise to the wee hours. Keep that in mind when determining how much to tip..."

http://www.yachtworldcharters.com/articles/luxury-yacht-charter-how-to-leave-a-crew-gratuity