A: After the great flood, the body of the Great Deku Tree from OoT floated to the surface with a small portion of the earth (in the root system) and the young Great Deku Tree Sprout. Because of the flood, the Great Deku Tree Sprout was uprooted and floated through the Great Deku Tree's mouth, which later becomes an entrance to Forest Haven. This is supported by the fact that the outer parts of Forest Haven are a grey colour (the same colour the Great Deku Tree becomes after his death). Additionally, the Great Deku Tree of OoT seems to be several times larger than the one in WW, taking the lower levels of the Deku Tree's inner dungeon. If the Great Deku Tree's mouth is not the main entrance, it is likely one of the higher entrances/exits (like the one you use to get to the Forbidden Woods).
B: The aforementioned situation happened, but instead the Great Deku Tree drifted away from the Deku Tree Sprout and became the Forbidden Woods. The Deku Tree Sprout proceeded to grow to maturity and created an outer trunk for protection from the hollowed out Great Deku Tree, still filled with monsters, and this barrier trunk later becomes the visible parts of Forest Haven.
I'd agree with what Ocarinaboy said but, I'd also like to add an option C. that the more I think about the more it makes sense to me.
C. The Goddesses sent people to the Mountain tops in Wind Waker, but if you think back to OoT the only mountain there really is in that game is Death Mountain. Obviously, there's a problem cause you got multiple Islands popping up all over the Great Sea that shouldn't be there, a prime example of this being the Forest Haven, and the Forbidden Woods. My idea would be that the Goddesses are responsible for all that happened with the Deku Tree rising to the top of the Ocean. He obviously plays a part in helping Link on his quest, and, the Goddesses knew that so they provided a way for him to be available, instead of being at the bottom of the big blue wet thing.
Also, the Forbidden Woods I always thought were the old Kokiri Forest cause you can find some of the Old Kokiri Houses. Forest Haven on the other hand, I believe to be the Deku Tree's Clearing, or if what Ocarinaboy said is correct, and the Deku Sprout was moved inside the Deku Tree in the flood, then it's Inside the Great Deku Tree, minus the top half of him.
You know, I can't explain the fact that the mountains appeared (Might I suggest C?) but there might just be the fact that the Deku tree in TWW is just the tip of the iceburg (Semi-literally; the tree may have it's roots at the base of the mountain where it formed.)