The NY Times had no ability to get permission from the original copyright holder because no one knew who that was. They republished the original article as an appendix/supplementary item to another article published in the physical paper (available online at http://www.nytimes.com/2012/02/04/opinion/nocera-the-cost-of...).
This is the textbook definition of "fair use": providing a copy of an out-of-print, otherwise unavailable news article, for the purposes of supplementing a published news article. (Fair use is a multi-factor test with no fixed requirements...it's basically whatever use is "fair" in the context of the actual use.)