The description for "Constructing a Citadel" says that "If the new culture border claims hexes owned by another Civilization, you will incur a diplomatic penalty as a result."
Does this apply to city states? Are they counted as Civilizations?
Yes, you can use a Citadel to steal tiles from an adjacent city state.
Just like with civilizations, doing so will result in a diplomacy hit, though unlike full civilizations, City States are much easier to bribe back into their good graces.
You will lose 50 influence if you are not allied with the City State. If you are allied, you will not lose any influence at all.