Panama City is where the country's trips are sold, including most of the ones that happen somewhere else — the Emberá villages on the Chagres, the day over the mountains to Guna Yala, El Valle, the canal, and the birding at Gamboa and on Pipeline Road.
The canal itself needs no operator: the Miraflores visitor centre is a taxi ride and an entry fee. What is worth booking is anything upriver or into the forest, where the boat and the guide are the trip.