For the most part it is extremely difficult, if not impossible, to map water. This is because when the water is moving it's impossible to get unique tie points between the imagery. You can however, map water if it is calm and there are visible features beneath the water such as a reef. Even with the visible features, it can be tricky to pull off. You can create a contour file of the shoreline, but because of the noise that will likely be introduced in the point cloud due to the water I don't know how useful the end file would be. Please let us know if we can help with anything else moving forward.