Just my two cents I think that the best tip you can give an owner/operator charter business is a good review/referrals/additional business.

So out of curiosity, if you were to charter with a big name charter company boat (Sunsail, Moorings, etc) for $7000 or 8000 for the week and hire a captain for the week for $2000 or $3000 (just using round numbers here), do you tip the captain based on the total amount spent? In this case the $2000? Or do you tip the captain a few hundred and go find the owner of Sunsail/Mooring and give them the rest?

I will say that most of the all inclusive owner/captained websites give you a total price and then suggest a 15-20% gratuity.