I try to keep my Nautical Level within 2 levels of my character level. It takes a little more work but any time my level is lower than I like, I attack ships while sailing to my quests till my level is up where I like it.
My suggestion is to go back to Skull Island and work your way up the chain (story line) until you reach ships you have trouble defeating and then go back to the prior area where you didn't have that much trouble. Make sure that you are not boarding them because you will sometimes get ship equipment that you can either use to upgrade your ship or sell to the Bazaar or vendor - whoever will give you the best price..
One thing I had to learn was that certain ship equipment can be used on all ships, so I move the best equipment to my newest ship. Always keep at least one type of ship (Pirate, Monquista, Cool Ranch, MooShu, Royal Navy, etc.) and keep the best equipment on them. That way you will always have some equipment that you can use on your next ship..
Right now my swashbuckler is max (Level 65) and has a really bad nautical level, only a mere 36!!!
Any help :(, I always struggle with nautical stuff since I have such a low nautical level
Hey Rachel id be happy to help you in game if we could arrange a meeting somewhere soon I'll just need ur pirates name. Btw you may not remember me but you replied to some of my messages and we were going to meet but I kind of got out of the game and now I'm getting back in with the new update coming out. Once again can't wait to meet you