The best thing to clean a boat carpet is: TAKE OUT THE CARPET!!!! Fishing boats should never have carpet on the floor. I took mine out and put in a vinyl floor. Never have to worry about cleaning the carpet again.
Now really, what to do is take it to the steam cleaning u-wash car wash, and use the soap in the pressure washer, and then rinse with pressure washer on rinse cycle. That's what I do. I did it this year, than decided it was time to put the vinyl floor in.