The initial call at the Marly Building Supply company came in at about 12:20 a.m., and firefighters battled the blaze for at least eight hours in brutally cold conditions.
Authorities say the fire was fueled by lumber, roofing, sheeting and other materials inside the building at 858 Meeker Avenue.
Adding to the difficultiies were hydrants frozen by near zero degree temperatures as the fire continued to spread.
Fire officials say the yard had both open areas and other small structures that complicated the firefighting effort.
"We did try to get some interior hose lines but were quickly overmatched by the flames and the fuel load, so we withdrew them for obvious safety concerns to our members," said Deputy Chief Brendan McSweeney.
Firefighters were finally able to bring the blaze under control by about 5 a.m.
"You are at a loss for words, and I feel for the people because I happen to know the owners," said neighboring businessman Francis DeVito, who says the company employed many workers.
"i think he started out as a building contractor and then expanded to what he held in these businesses here," said DeVito.
200 firefighters and 50 pieces of apparatus including marine units responded.
There were no reports of any injuries.
The cause of the fire is under investigation.
The Brooklyn-Queens Expressway was briefly closed twice due to blowing flames and ice spread by the hoses.