by Webhead123
Obviously not an "official" answer but just the way I think about it:The monsters being more interested in smashing and dominating Tokyo City than Tokyo Bay, I assume that most of an attacking monster's efforts would go toward taking the city (the monster in Tokyo Bay is just in the way). As such, we play that the monster in Tokyo City decide first. In our case, if the city is yielded but not the bay, the monster who just attacked enters Tokyo City while the monster in Tokyo Bay stays where he is.
I say that Tokyo City is the primary target because a) once the number of players drops below 5, Tokyo Bay is ignored and b) in Godzilla movies, the bay is almost always just a short-lived and unfortunate casualty as the monster(s) stomp their way toward downtown Tokyo.