Can both monsters in Tokyo yield at the same time after an attack?
Yes. From the rulebook:


  If the monster in Tokyo Bay is attacked it can choose to abandon Tokyo Bay. In this case the monster that attacked must move in unless it is moving into Tokyo City, in which case Tokyo Bay becomes temporarily unoccupied.


If both monsters yield, as this indicates, the attacker would move into Tokyo City and Tokyo Bay would become temporarily unoccupied.