Is it a specific spot the game crashes, or just whenever you get close to the harbour?
Can you take the path into the harbour in human form? From the slayer camp you can swim out to the far east and try transforming once you get outside the ant-dragon shield (2 of the hunting quests are near there, on either side of that channel).
There is an auto-save triggered a little way down the eastern channel. If that is where the crash is, you could try swimming, rather than flying, and see if that makes a difference.
Had you previously been able to fly by that particular spot? If you keep multiple saves, try loading the oldest one you have after getting the battle tower, and see if you can fly by the harbour.
If the problem is in your latest saves but not in an earlier one, then it may be a problem with the save itself (triggering a particular cutscene, or something). If it is consistent, then the problem may be with the game itself (such as a corrupt texture, etc), in which case it may help to do a clean reinstall of the game.
First Aid Kit for Divinity IIFirst Aid : when Div2 does not start or crashes