Yes, the Prospect Plantation and Dunn's River Falls excursion does pass through Fern Gully -- though IMHO Fern Gully is no big deal. The plantation and the falls really are the highlights of the trip. They are far enough from the city of Ocho Rios so you will get to see some of the countryside, but not so far that you will lose a lot of time in transit.
I don't have any specific recommendations as to other things to do in Jamaica. One of the shopping centers is within walking distance (basically a long block) from the pier if you want to spend more time shopping than the tour allows. In the past, I have been quite content to return to the ship to relax and perhaps to go for a swim in one of the ship's pools.
I really did not see any interesting lunch spots ashore, so it's natural to return to the ship for lunch. Also, you probably will want to change out of your bathing suit before going back into town. After you get lunch, your time will be somewhat limited (probably about two hours or so) so don't plan anything too ambitious or far.