The ruling puts the case on course for trial as soon as January.
Mitchel Alvo, Salvatore DePaola and Jeffrey Melofchik - the only people criminally charged in the deadly August 2007 blaze at the former Deutsche Bank building - have pleaded not guilty to manslaughter and other charges.
Prosecutors say the men knew about, failed to fix and even covered up a break in a crucial firefighting water conduit, called a standpipe, and that was a critical factor in the firefighters' deaths.
The men, who were working to dismantle the toxic tower, say they were unfairly blamed for a fire fueled by others' failures. They asked a court earlier this year to dismiss the charges.
Manhattan state Supreme Court Justice Rena K. Uviller noted that the raging fire was a result of a range of actions and inaction, from a worker's careless smoking to the fire department's failure to conduct required inspections. But the allegations against Alvo, DePaola and Melofchik represent enough of a role in the tragedy to sustain their indictments, she wrote.
"Although there were several factors contributing to these fatalities, the grand jury reasonably inferred that defendants' conduct in dismantling the standpipe and the failing to take corrective action was an actual contributory cause of the deaths," Uviller wrote.
Melofchik lawyer Edward J.M. Little declined to comment on the ruling but said his legal team was "looking forward to the trial, when our client Jeff Melofchik can finally have his day in court."
DePaola's lawyer, Rick J. Pasacreta, said he was confident DePaola would prevail at trial. Alvo's lawyers had no immediate comment; nor did prosecutors.
The World Trade Center's south tower collapsed into what was then a bank building across the street on Sept. 11, 2001. The impact heavily damaged the bank building and filled it with toxic debris. A laborious process of dismantling the now government-owned building has taken years.
On Aug. 18, 2007, a construction worker's discarded cigarette sparked a fire that tore through several stories of the building.
Firefighters contended with a roster of hazards, including deactivated sprinklers, stairwells that had been blocked to contain toxic debris, an air system that was supposed to control toxins but ended up concentrating smoke, and the broken standpipe.
With the standpipe severed, it took 67 minutes for the firefighters to get water by other means to fight the blaze.
Firefighters Robert Beddia and Joseph Graffagnino became trapped on the burning 14th floor. They died of smoke inhalation after their oxygen tanks ran out.
The standpipe had broken during asbestos removal work in the building's basement in November 2006, Manhattan prosecutors say.
Alvo, the director of abatement for project subcontractor John Galt Corp., and DePaola, a Galt foreman, ultimately had a 42-foot-long section of the standpipe cut up and removed from the building, according to prosecutors. Melofchik, the site safety manager for general contractor Bovis Lend Lease, filled out checklists saying the building's fire suppression equipment was working despite the broken standpipe, prosecutors say.
"While (the three men) choose to point their fingers at other entities who they claim bear responsibility for the deaths of the two firefighters, this case is about these defendants and their actions that caused two deaths and nearly caused numerous others," Assistant District Attorney Noah D. Genel wrote in court papers in May.
Defense lawyers say the men didn't realize the pipe was a standpipe - and they note that a raft of inspectors never flagged it. Regardless, the attorneys argue, the broken standpipe wasn't the key cause of the firefighters' deaths. They point to the many other perils and oversights that prosecutors and city officials have acknowledged.
"Why are they scapegoating a few defenseless people at the bottom of the line?" Little asked Uviller at a hearing in July.
When the case was unveiled in December 2008, then-District Attorney Robert Morgenthau pointedly said there was blame to go around among the maze of government agencies and companies that had worked at the building during its dismantling.
The city agreed to fire safety reforms, and Bovis agreed to pay the firefighters' families $10 million in a memorial fund.
If convicted, Alvo, 58, DePaola, 56, Melofchik, 48, could face up to 15 years in prison.
Galt also faces the same charges and has pleaded not guilty. The company is seeking a separate trial.