I have exchanged email with the CP worker who asked that the UberCache be removed. He explained that his job is to look for and remove anything that looks like it is being used by homeless folks as shelter or a stash in the North Woods. He further explained that large objects frequently float along downstream until they jam up a drain or underground passage where the water must continue on. This causes quite a bit of trouble and flooding during rainstorms. So they try to remove any unnatural objects anywhere near the water. He said that he did not know of any policy about geocaching either way, but that he contacted the CO because he felt that type of container could not remain at that location. He doesn't know of any other caches in Central Park and hasn't searched the web site for them.
So we should all be safe.