Actually, the NYT referred to him as Mr in every article about him. They always refer to the President as Mr. It’s not some sign of extra respect towards Obama.
You can go back to their archives and it was always Mr Reagan, Mr Clinton, etc...
There’s plenty to get on the nYT about but this isn’t it.
In fact, when they did it with GW Bush, many Republicans took it as a slight, not respect; they wanted him referred to as President Bush, but many in the media simply called him “George Bush” or “W”.