If you're looking for a modern take (spaceships) I'd highly recommend the little (but huge) indie game Star Sector. Huge modding community. Insanely easy to mod, even on macos. I have a bunch of scifi games that scratch the itch well, although they don't often give you the feeling of being the actual ship captain who walks around towns, tries to seduce governor daughters, etc. Most of them you build a crew and aren't directly roleplaying the captain in the same manner. Star frontier.. I probably have 10-20 games on steam that capture the feel to a point.

I can't say that I own any good modern pirate ship games other than Black Flag, and I'm not sure that counts here, I didn't play much of it.