So, I understand what you meant by "actual operators". Actual operators refers to the boat operators who actually operate the boats. Now, as you pointed out there are two which are fairly common and famous, i.e.
I found two more which seem to have their own ships based on the obscure information available on the internet.
Aventuras 2000 is also another local tour operator which has a wide variety of tours which seem to be more oriented towards groups. They have a large number and some great reviews on TripAdvisor.
Pesantez Tours is another local tour operator which has some good tours designed for a larger number of people instead of the more personalized ones offered by the others. Unfortunately as one would expect, their site is in Spanish. They have a half day tour of the canal and city tours as well.
Leaving these two apart, I found some more which are well known and appreciated for their more natural and customized tours.
Ancon Expeditions as the name suggests offers expeditions and customized tours within Panama and the Panama Canal as well. They have been praised on TripAdvisor by some top contributors which makes me believe they are quite legitimate in terms of a good experience. They have a site in English fortunately.
Panama Canal Boat Tour offers some tours in small groups as well as expeditions in kayaking, fishing or simply nature.
I also came across a local tour operator called Rene who operates a site called Your Man in Panama. His efforts have been acknowledged by some on TripAdvisor. Unfortunately even he does not provide the big ship tours because the number of people who do this are very restricted. But I do suggest contacting him for detailed information about any more "actual operators".
There is a good list which highlights operators outside Panama as well and some more inside Panama but which probably do not offer transits. This list might be good to look at for someone planning a cruise.