I don't have a subscriptiohn for the NYT, so I can't compare. Plus I don't have a Kindle. Plus my news get formatted in epub.
The news come with a main menu, then first section menu, articles, second section menu, articles, etc. At the beginning and the end of each section menu and article there are links to jump forward and back and to the appropriate menu.
Plus there is a navigation bar at the bottom of the page, which offers divers buttons (depending on what is displayed at the moment).
No columns here, but the links and buttons provided offer - in combination with touch - very fast and efficient means of navigation.
EDIT: But actually, aren't we getting a bit OT here?
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