Sort of hard to answer........
Couple of questions for you.
1) What type of water is the dead whale in? Cold, Warm? What is the climate of the harbor (Carribean, Easern Sea Board?)
2) How big was the harbor? fundamentally what happens with any type of dying organics in water is that they are broken down by bacteria - Organic > Nitrite > Nitrate > Ammonia so if the Harbor was sufficintly small, the Ammonia could have precipitated a total harbor kill - thus accelerating the breakdown as additional fish, molluscs, crustacians etc dies. (Most sea creatures are very intollerant of ammonia - especially reef based animals)
However, taking a moderatly warm harbor of large size (Say like the Old Boston Harbor) afte 4 months the vast majority of all organics will be gone.
Example: Clown fish dies in a coral reef - 2 days nothing but bone
shark dies in a coral reef 1 week to reduce down.
As the water gets warmer, the breakdown time increases.
Hope that this helps....