Unfortunately, you don't have many good options. Any paint on goop will not last, especially in high-stress areas.
One option that will work is getting another batch of goop, adding pigment (from art store) to it, and re-coating the boat with it. Goop is one of the few things that sticks to goop. You will need a lot of dark pigment to make a noticeable difference, and the final result will still be uncertain, not to mention the boat will be heavier (but stronger). If you are desperate, consider doing just deck (since you look at it all the time)
In reality, your 2 best options are a) live with the color - maybe you will get to like it, or b) reskin the boat over again,