This is the first time we are using Ed Hamilton & Co to find us a boat. They are very good at helping compare the relative value and reputation of every charter operator in the BVI. You don't pay more, they get a cut from the operator.
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As a general rule, I believe you get what you pay for. Big operators like Mooring do have a premium for the "brand" but its not as high as some complain. You know what your getting and know they will be there. They have newer boats and plenty of replacements, if something went wrong. The providers that charge half are offering a much lower grade product, usually in terms of the boats age, visible wear and tear and resultant reduced reliability. Or, they have a very limited fleet and you risk being stuck, if your boat has a problem. That doesn't necessarily make it a bad idea, you just have to know what you're getting and accept the risk. You can come up craps on any boat. Our last bareboat was less than 6 months old and didn't even have a name yet and stuff was broken.
We've only chartered from the Moorings, but have many friends that have used others with widely varying experiences. I'm going to throw out a gross generalization and say you could save about 10% to get the same quality, fleet redundancy, etc with a comparable competitor. Once you find cheaper, you are getting cheaper. Again, that may be okay.
So far, Ed Hamilton & Co has been extremely helpful in sorting them all out.