Wellington would also be affected, along with the coast south of the Taranaki Bight. Christchurch and Dunedin would be under water, and Southland and Stewart Island would shrink as well.
The interactive maps published by the magazine show how the world would look if all the ice on land melted and drained into the sea, raising sea levels by 66m.
Niwa chief climate scientist Dr David Wratt said New Zealand would definitely be affected if the polar ice caps melted.
He said the latest Inter-Governmental Panel on Climate Change report's highest scenario led to a sea level rise projection of 52cm to 98cm by 2100, compared to the late 20th century.
He also said the IPCC report indicated global warming above a threshold of a few degrees could lead to the near-complete loss of the Greenland Ice Sheet over a millenium or more, causing a global sea level rise over that 1000-year period of about 7m.
New Zealand would "certainly" see a similar rise around its coastal and low lying areas if that scenario were to play out.
To view the National Geographic interactive map look here.