You'll pay the same or more than booking on the cruise line, you won't get the security of a ship's tour, and you'll probably end up waiting around for hours while they "put the tour together"... with shorter and shorter port times, I'd hate to be standing around waiting anywhere...
Actually my did a tour thru one of these companies because we had some extra time. The price was cheaper than the same tour on board and they were fast. I went up the Mt Robers Tram while she di the fish Hatchery and something.
Not saying they are the way to go, just saying the way it was.