The president was not at the tower when the fire started and he has not issued a statement on the fire as of 8:55 a.m.
But smoke continued emanating from a rooftop heating and cooling unit of the 58-story building, fire officials said.
Numerous fire engines responded to the early morning call at the Fifth Avenue building, with one picture showing more than a dozen vehicles attending the incident.
According to Reuters, one fire-fighter received non-life-threatening injuries from the fire.
The president's son Eric later tweeted his thanks to firefighters for doing "an incredible job".More news: Expect specific action on Pak. this week, says US
'The men and women of the #FDNY are true heros and deserve our most honest thanks and praise!'
The Fire Department of NY said it was called there at around 7am (noon GMT) after the blaze was reported on the top floor.
People posted video and images to social media, showing smoke rising from the building. Flames coming from the vents.
Firefighters are on the scene along with members of the NYPD. Two minor injuries are reported; a firefighter who was hit with falling debris and a civilian.