There appear to be several operators that do just the canal tour. This seems to be a fairly typical example. You get to board the boat at the Flamenco Marina or Amador Causeway (both near Isla Perico). The only bus transfer is to get you back from the far end of the tour: partial tours end in Gamboa, so you will need some kind of transfer. There is no breakfast, but there is lunch provided. It's a 5-6 hour tour so you'll need it.
We did this tour, booked through a hotel, and booked only a few days in advance. The boat waited for a specific start time, so I'm guessing that if you showed up with a credit card you would probably get on. In any case I would expect that booking the previous day would be acceptable.