Corsair series by Fuuko Minami
This is a 3 volume yaoi manga series that isn't yet available in English. I read the scanlations online, and I bought them in Japanese, because, even though I am not fluent in Japanese, the series was so good, I wanted to possess it, even if it's not in my native language.
The story is rather heavy, though there are a few light hearted moments, and the ending is happy, the ending scene being very touching. The main character, Canale, was blinded when he was young, but that doesn't stop him from being a skilled swordsman. He has lived a very hard life, and he is a very well developed character. His partner, Ayace, comes across as very aloof and stand-offish at first (he's a cool, suave pirate), but he in fact deeply cares for Canale. After many trials, and his past coming back to haunt him, with the help of Ayace, Canale is able to make peace with himself, and yes, the two sail away together. Again, the last scene is very touching, with Canale saying he wants to see Ayace's face. Ayace brings Canale's hand to his face and says, "I'll teach you." They kiss. I keep going back to that scene because it is just so sweet.
There is a spin-off manga called Corsair: Eigetsu. It is just one volume as far as I know, and it follows another one of the characters from the main series. I hope this series becomes available in English some day, because I recommend it to any yaoi fan.