Agree 100% with the other posters. Comfort tops everything, so that you can truly enjoy your excursions and your time on the ship. I'd bring the grey Brooks running shoes, since you know they're comfortable after many hours. If your clothes are mostly black and white, grey will look just fine. You could throw in the white Keds, as well; if they have a platform of any type, or extra cushioning, they could be fine for shorter excursions or around the ship with the dress, for example. And then the black sandals for evening now and then.
If you look around the ship and the ports, I'm guessing you'll see a lot of women who have some version of a running shoe on. No one will think: "Look at that dorky woman!" They'll think: "Look at that smart woman who has on the right footwear!"