If you've ever noticed all harbours are behind wave breakers. Otherwise the boats would bang against each other and do a lot of damage. So no, not when you're moored.

When sailing that's another matter..

I've never lived on a boat, but I spent a few weeks sailing the Mediterranean in high school... After a few days you don't really notice the motion that much unless it gets really rough.

That being said, I'm not predisposed to sea-sickness anyways, so I may be a bad data point; my point is just that it seems that your system adjusts to the constant motion (you know, getting your sea-legs and all that).