Archaeologists at the World Trade Center site have discovered a nearly 400 year old ship buried underneath the WTC complex.  The ship was most likely deemed un-seaworthy and sunk intentionally in the early American colonists efforts to "build up" the islands shore line. Almost the entire WTC complex was once under the Hudson River.

The discovery was actually made last July, but was reported yesterday by Fox News in an article that also explained how Manhattan Island's southern tip was "built up" out into deeper waters, making it an ideal port for large ships and eventually it became the most important port in the world.

The land was filled in little by little, creating all but a sliver of the original 16-acre World Trade Center site. Both of the Twin Tower footprints would be underwater if the shoreline still looked like it did when Manhattan was discovered in 1609.

This article from archaeology.org gives further details on the history of Manhattan Island.

Here is a map of Manhattan Island in 1660.. compare to the picture below of a map from 1874.

A Colonial Map of Lower Manhattan. (Library of Congress).

The above photo, from the Library of Congress, shows the lower tip of Manhattan as it was in 1874. By this time, early Americans had already began "building up" the shoreline around the southern tip of the island, eventually extending the island out into deeper waters.

This Google map of modern day lower Manhattan shows the World Trade Center footprints. Most of this area was once under water.