Here is what I did:
Pull everything you can out of the boat. Vests, anchors, ice chests, etc. You need as much ventilation as possible to let it dry out.
Then make sure you will have non-stop sunshine for the next 48 hours.
Fire up the vacuum and give the carpets a good cleaning(no point in trying to scrub the carpet if its not already free of debri).
Next fire up a pressure washer and take two or three passes through the interior. Note that its REALLY important to excersize restraint here. You dont want to put a hole in the carpet because you turned the pressure up too high. Just enough to move the fibers of the carpet around a bit.
Now take a NEW auto tire scrubbing brush (stiff bristles) and some soap of your choice...scrubbing down the carpets once or twice.
Now grab a shopvac or steam cleaner and such up as much of that dirty water as you can. You will be AMAZED at how fithy the water will be.
Finally, rinse it through with the pressure washer another time or two. (I have never tried fabric softener, but I like the idea).
Now let the boat sit out in the sun and dry for a good 48 hours plus.