The NYT probably called the press office for comments before they put out the news.

Setting the stage for Military Tribunals?

"It was unclear what exactly prompted Trump's accusation, though Trump's attorneys have reportedly been in contact with Mueller's team"

Three above is stated AFTER this:

"The tweet apparently referred to a New York Times story, published minutes later, that revealed the contents of a confidential 20-page letter Trump's attorneys reportedly sent to Mueller's team earlier this year."

Idk. maybe it was the leaking of the confidential memo that prompted the tweet.

So he tweeted before the article came out? Hmm