I changed the ship's layer blending mode to "Darken". Some additional changes were made in order to improve brending, such as increasing brightness, decreasing contrast, erasing the borders and adding soft blur.
Some further touches were done to the ship, to give it an old and worn feel. I also played a little with levels and some other settings for the whole picture.
The first pirate comes in. Removing the black background was very time consuming, and I had to clone some bits to fix his elbow and sword. The results of this can be seen in the next step.
The rest of the crew shows up. At this point, I've experimented with several different settings in order to make them blend better with the background, with variable degrees of success.
Almost by the end, I decided that I wanted to move the background a little upwards, so more of the ship could be seen. After this step, I only applied a cold photography filter, plus some other final touches to give the final result.