The duty varies depending on the item, but 20% is what it usually is. I would access Belize's customs website to make sure. On top of the duty you have to add 10% GST, and another 7-8% for envirmental taxes and other fees. So you'll pay around 38% of what you paid for the item in the US (plus shipping), not the value of the item in Belize.
The best way to ship is through Miami as Pug said. It's hard to find ebayers that'll deliver items to a non-confirmed address if using paypal, but a boat might be different. Take it to Hyde Shipping - Medley, FL. 33178. It will then float to Belize City and be ready for pickup about a week after you sent it. Get a broker, have all documents ready, and it's usually pretty easy to clear the item. Then you can barge it to San Pedro, or just drive the thing out there.
I'd estimate shipping cost from Miami to Belize City to be between $700-$1200, but you'll have to check that out yourself since I have no clue what size the boat is. A jet ski would be less.
Hope that helps.