That's neat !!! Gorgeous map !!!
For the boats, I think you can use the same little boats that are on you previous map : I don't think that a large boat can enter this far in this partially underground river...
So, I think it would make sense to imagine that there's a harbour on the mouth of the river, where all the goods are transborded on small rowing boats (like the ones you already draw) and those rowing boats are going back and forth between the city and the harbour. What do you think ?