If you are self-employed and the boat is used in your business (example: a fishing charter boat), the tax would be deductible on Line 23 of your Schedule C.
If the boat is not used for business, and if you itemize, the registration fee would be deductible on your Schedule A (subject to the IRS limitations on deductible local taxes), but only if the fee is determined by the boat's value and not by its size. age, or some other factor.