There are silicone products you can get for pouring into moulds, if you were to put that in a dish the same diameter as the base of the bong and then set the bong in it it should fill any holes, or if you can keep it from sinking into it too far it'll add a new solid layer of silicone to it blocking any leaks. You should be able to find it at any hobby shop, comic stores where they sell those tiny model things geeks paint (not judging), or amazon.
Or a more specialized store, like they ones where you can get latex body paint.