As far as I know there is no regular ferry connection and hasn't been for decades. The "standard" way i.e. how many backpackers do it, is to travel on a sailboat from Portobelo (Panama) to Cartagena (Colombia), visiting several spots in Kuna Yala (a.k.a. San Blas Islands) on the way. This has become quite popular, and there are several boats going back and forth, taking passengers. I haven't done it myself, so can't give you any useful advice about the cost and how to find these boats. (Google is your friend, and there will also be guesthouses in Portobelo that can help.) I would reckon that it's more expensive than a flight, but you are spending several days in some of the most beautiful places in the Carribbean which would otherwise be more difficult and expensive to reach, so it's probably worth it.
