Im about to sound like a huge nerd, but there has been some debate over the relations of the three games. I see it like this:

Some people think these timeperiods are totally different, but it is possible that the Great Sea, the ocean from PH(forgot its name), and the ocean realm from ST are all connected. At the end of WW Link and Tetra go out to find new land, and many years later, their kids get into trouble with the Ghost Ship and Link meets Linebeck I. Later, when Tetra is saved, they go exploring farther, probably to found New Hyrule. Later, their kids come in and explore the land, which are the events presented in ST. This explains how Niko is still alive, and how there is a Linebeck III. I may be wrong, the timeperiods between may be many more generations, but this is how I view it. The overall time between WW and ST may be about 100 years.

Heh, so there ya go.

*EDIT*
I found the greatest Christmas card in the world, even if its after Christmas.
*EDIT*