Brandon, That sucks.
Did you sign anything regarding the condition of the boat prior to the authority in question taking it?
Generally, when towing/storing a car, a form is filled out noting damage, overall condition, etc. The office in charge of the investigation signs that form prior to the towing agent taking the vehicle. Any damage beyond that which is present whe they take cusotdy of the vehicle is on them....In Ca. that form is called a DMV-180...If this is the case, take a look at that form, take lots of pics and speak to an attorney.