I know it's cliche, but you could use a solar panel, there's a lot of variables on the water when it comes to wind. Specifically how are you going to manage your windmill extracting energy from the motion of your boat when you're trying to get somewhere (relative wind from the boat's driving through the air), and what are you going to do when there's a storm?
If you're concerned about system longevity, you should consider a Lithium Iron Phosphate (LiFePO4) battery which has a cycle life of 2,000 (capacity degraded to 80% of original) but it comes with the added complication of needing a Battery Management System to keep the cells balanced. Otherwise a deep cycle lead acid battery will work great but may only last a year if it's cycled every day (cycle life is around 300, again this it to 80% original capacity). Regardless of the battery choice, you'll want a low voltage indicator on your battery to protect the battery from overdischarge and give the Pi time to gracefully shutdown to prevent data corruption.
For some intuition on how a self-contained system might work, this is a site hosted from a raspberry pi running on solar/battery power. It explains some of the configuration: https://solar.lowtechmagazine.com/about.html
You're going to have to know how much power generation time is available per day (to determine the turbine size) and how long you need the Pi to run without replenishment (to determine the battery size). This site will give you an idea of Raspberry Pi power usage to help you size your battery and wind turbine/solar panel.
If you're looking for the ultimate green solution, you should really just wire your inverter (from wind or solar) directly into your boat's electrical system and power the pi out of a normal outlet. I know I know, that defeats the purpose, but it'll actually be more "green" because you won't lose energy in the battery charge/discharge cycle since it'll be used immediately (best case scenario you'll probably get around 80-90% energy back out of a battery) and you won't miss out on energy that is being generated because your battery is full and the Pi is only sipping a few watts.