The best place to be in terms of feeling less movement of the ship is lower down, in the middle of the deck.
Having a window is always nice, not only to see out, but because it lets the light in. If you're in an interior cabin, being higher up or lower down doesn't matter except in terms of feeling less movement.
The bottom passenger deck is still above the water line, but sometimes engine noise can be heard from that deck. The second deck up, whether you have a window or not, is a good idea, although you'll still hear anchor chain noises on that and several other decks. Usually there is just a small price difference to go from a window room on Deck 2 to a window room on Deck 3.