If you want a different underground river tour experience than the standard one, with a more native flavour, you can try Joseph, who lives in Sabang. Unfortunately, he has proven to be unreliable, but there are a couple of chaps with a booth set up on the beach, perhaps you could ask them if they offer the same.
The standard tour goes about halfway up through the caves, the boats not permitted to explore the remaining 8km. As shown in the video near the bottom of the Puerto Princesa page, the boats are a constant assembly line going in both directions, although you might end up seeing more than with Joseph.
For 500p Joseph will guide you through the jungle to a cave entrance past the point where the regular boats are allowed to go. And if you decide to stay overnight in town, he can offer you the following options: 500-800p basic rooms, 2-5,000p for aircon, electricity 24/7.
The entrance to the cave, where the source of the river starts. Joseph was one of the pioneer guides before the tour became famous, but no longer likes it because it is busy with too many tourists. From the river’s source he can take you deep downstream. Note that it is a maximum of 1.5 hours walk each way, and there is some tough climbing, so not for young children or the elderly.
Having not met our contact, at least we took some videos of Sabang: