Carts can be loaded onto longships now with minimal risk, same with animals at least in my experience. Your handling sucks, but it works.

The cartcrate option is safer, if a bit more tedious. It does still work as the boat's collision box interacts with the cargo crates, however you still run the risk of destroying the crates with collisions, and then all your non floatable goods become offerings to posideon. I would recommend just trying the cart method first.