It wasn't just the NYT website. According to sources at the paper, the nytimes.com e-mail server also went down.
One report, from Fox Business News, had stated that the corporate and media sites of The New York Times were experiencing a major cyber attack. That was not the case according to the NYT. “The outage occurred within seconds of a scheduled maintenance update being pushed out, and we believe that was the cause,” said Eileen Murphy, a spokeswoman.
Specifically, according to a source close to the NYT, the primary cause for the outage was due to bad firewall configuration change that blocked all incoming traffic and for some reason the IT staff wasn't able to rollback the change.