What town are you in? Any DMV office that does plates should be able to register your boat. Many town clerks can do it too. A lot of places that are agents for hunting and fishing licenses can also register boats.
The state wants you to go through them because they keep the "agent" portion of the fee. You might want to go that route if your town does not have any boat related expenses. You'll know your funds will chip in to the programs you use.
Good luck!
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