Here's the latest update from my recent trip to KK last Nov. The refurbished jetty called Jesselton Point
(ex Sabah Port terminal) should be able to arrange for the island trips (Manukan, Sapi, Gaya, Sulug, Mamutik). The boat price seems to be regulated by the authority and it depends on how many people sign up for the boat trip.
Otherwise, yes, there are hundreds of local travel agents are advertising similar service from the hotel lobby or shophouses around town. All of them have to depart from the same jetty, mostly.