I think I rmember the Boss key being in the room where you fight the Moblins. It has a gate (behind it is the chest) and there are a bunch of crystals to hit all around the room. You go to the central hub (the room with the giant hanging flower) and cut the vines with the boomerang. When you hit the bottom you hop off of the flower onto the moving platform and use the Deku Leaf to go down the hall. Eventually you will reach the room. This is for the Forbidden Woods...... I think.
I don't believe there is a Boss key for the Forsaken Fortess..... Actually I PRETTY sure there is not one.....
BUT! Do what S.Mario said and check out the Zelda Dungeon WindWaker Guide. I'm pretty sure I remembered it correctly, but you can clarify if you want to.