Regardless of where you stand on tipping or how much, I don't think it matters if they are owner/Captain or just crew. Even if they are the owner and saving on the cost of paying a crew, they are the crew and doing the same work a crew would do. So while an owner who hires a crew pays more, they also don't deal with guests for a week.

I like Mike's suggestion though of basing it off of what the labor would cost. I don't know why it should be based off the cost of the charter.

If I leave a tip in a hotel, its not based off the cost of the room - two rooms could differ in price by a couple hundred dollars, yet the effort involved in both would be the same. I'd say its very similar for boats too, only difference is when you increase the number of people.