It depends on if you are a passenger or the driver.
If you are driving the boat yourself, then you say you are driving the boat. This is more common if it is a small private boat, and you have the training to drive it yourself.
If you are riding in the boat while someone else drives it, then you say you are riding in the boat. This is more common when it is a large boat, like a ferryboat, that you pay to ride across in. Or if you are invited to spend time with someone who has a boat, so they drive it but you only ride on it.