How specific is this ability?
If a player wanted to use this ability with a gnome (Alternate Racial Trait) in the Skulls and Shackles campaign and choose ocean as the terrain; would they gain the AC bonus while on a boat?
Same with ruins in a forest if forest was the terrain type?
Bonded to the Land states that you select the terrain from the list of Ranger Favored Terrain options, so your real question isn't about bonded to the land; its about Ranger Favored Terrains. I would start by using the search feature to make sure that no one has answered this sort of question on favored terrains yet.
As a GM, personally I would make the call based on what the conditions of the environment are and because the examples under Favored Terrain are so broad, its only natural that you are going to get some overlap and there isn't a hard-or-fast rule that is going to apply in all situations. For example, if you're in a city that consists of many house-boats bridged together into streets and whatnot, I could see counting that terrain as both urban and water. However, if you have a city like New Orleans that is only built on top of a marshy area and the roads and buildings itself are relatively free of a marsh's terrain features, then that would only be an urban terrain instead of urban and swamp.
So, for your examples, I would say that being on a ship counts solely as water terrain while ruins would probably be urban; possibly underground if the ruins are dungeon-like and forest if the ruins are so ancient that the forest has begun to overtake them, breaking down walls and the roof.