What's great about watercraft compared to airplanes is that cities usually have a port right next to the center, while the airport is usually far away. A helicopter is somewhere in the middle, it can land to an industrial port or other area with less noise constraints. I guess e-vtol could solve that too if it's not too noisy?
Seaplanes are sometimes used in such situations, as in the area around Seattle and Vancouver (or perhaps, given the context, that should be the Puget Sound - Strait of Georgia?)
My only experience with hydrofoil travel was from Naples to Stromboli. The weather was good, and with wave heights lower than the hull clearance over the water, the ride was smooth.