Many lanchas, or small boats, provide transport from village to village around and across the lake. Some boats are scheduled like buses, other will go as soon as they accumulate enough passengers, like share-ride taxis. Generally the prices are Q3 for one harbor, Q5 for two, and up to Q10 for many or across the lake. The crew are a bunch of really unpleasant scoundrels however and will extort up to Q25 out of anyone with a light complexion or limited spanish.
Some people suggest it is generally best not to mention a price until you get off the boat, that will usually get you into the extortion situation, however. You can also ask the people with little or no luggage how much they're paying chances are they're at least a little familiar with the system. The prices are fixed and the locals or regionals always pay the same.
Examples of typical prices:Pana to/from Santa Cruz - Q10-Q15Pana to/from San Marcos - Q10-Q20San Marcos to/from Santa Cruz - Q0-Q15