You are almost undoubtedly thinking of the comic adaptation of Splinter of the Mind's Eye, based on the novel of the same name and included four issues published by Dark Horse and later Marvel Comics.
I haven't read it in years, and don't recall wooden ships specifically, but there was a swamp/water world, and Luke/Leia had more of a romantic relationship. It took place between A New Hope and The Empire Strikes Back.
The original book was published in 1978, and the comic adaptation was released between 1995 and 1996.
Splinter of the Mind's Eye was an interesting production, as it was originally written as a back-up sequel to Star Wars. In the event that Star Wars was not financially successful enough for Fox to pick up the sequel, Lucas wanted a sequel that he could finance and produce himself on the cheap. This led to Alan Dean Foster being hired to write a sequel separately with little input from Lucas himself.
In an interview with Yahoo, Alan Dean Foster explained the situation:
My contract was originally for two books: the novelization of the first film and then a sequel book, because George — being a student of Disney, I’m sure — wanted more material in case the movie was a success. He wanted something out there that the hoped-for fans would be able to enjoy while he was busy making the second film. The only restriction placed on me was that the follow-up novel had to be filmable on a low budget. That’s why I set it on a fog-shrouded planet. A lot of the action takes place in the fog or underground, which facilitates shooting with cheap backgrounds. The book originally opened with a fairly complex space battle that forces Luke and Leia down on this planet, and George had me cut that out because it would have been expensive to film.
Wookieepedia describes the end of the novel:
The two Yuzzem, Hin and Kee, never return. Luke wonders why, but then is crushed by rubble that fell from the cracking, ancient ceiling. Darth Vader then enters the Temple of Pomojema after having turned off the droids and killed Captain-Supervisor Grammel, Kee, and supposedly Hin. Leia takes up Luke's lightsaber and begins fighting Darth Vader, with little success; she is badly injured. Hin, badly injured, shows up and lifts the big rock off Luke's leg. Luke then fights Darth Vader, engaging Vader on a level which even surprises the Dark Lord. Here Vader conjures a ball of Force energy (possibly his own interpretation of Force lightning), which Luke manages to deflect. They continue to battle and Luke, his actions guided by the spirit of Obi-Wan and his power augmented by the Kaiburr crystal, strikes Vader's sword arm, severing it. Undaunted, Vader picks up his lightsaber with his remaining arm, and again pursues the exhausted Luke. Vader, also exhausted, is about to win, staggering as he approaches to make the killing blow, and he falls into a pit; Luke senses that this does not kill Vader. As the story ends, a healed Leia and Luke drive off with their droids and with Halla into the mists of Mimban, ready to take on further off-world adventures.