Puerto Rico is under the US flag so there should not be any custom duties to pay. Purchasing a boat there or in the US Virgin Islands is something to consider as the USVI is under the US flag as well.
Are you going with just your toothbrush or taking the house with you? If it's the house, or at least the contents, you'll probably use a container. Break your boat down and ship it with the household goods. You could also tow it to Florida and ship from there to reduce shipping costs.
If you're looking for a crew to sail it over, let me know! That would be a great adventure and a pre-runner to the Cuban Race thingy someone tried to get going a few years back..
I've lived in both PR and California you will love the sailing in PR and the islands. You can save some room by giving your wetsuits away you don't need them anymore.
Shipping to PUR is a piece of cake. I once shipped a drill rig, two support trucks, and fifty pallets of supplies to Aguadilla. They went out of Jacksonville.