I am not sure what room you are talking about, but if it is the room shown in the screenshot below, that chest cannot be opened until you get the flippers. It only has 200 rupees in it anyways. To get the boss key, you are going to need three normal keys. From the entrance, go downstairs, south, south, west (through the top left door), west, south, south, east, south, east through the locked door, shoot the statue in the bottom right corner with an arrow, use the last two keys, and go north. Manuever around the traps and go down the stairs to get the Boss Key.

