Trench, 43, was shot in the face and neck as he sat in his patrol car on May 28, 1985.
Prosecutors called his murder a case of mistaken identity. They said Santiago held a grudge against another officer who had been driving the same patrol car in a previous shift.
Defense attorney David Rudovsky told jurors that investigators zeroed in on that theory from the start and shaped their case to fit it. He pledged to appeal.
"He continues to assert his innocence," Rudovsky said.
The jury convicted Santiago on Tuesday after six days of deliberations. Jurors had to weigh evidence that was largely circumstantial and testimony from witnesses who had changed stories or details in the last 23 years. The weapon that killed Trench has never been found.
An appeals court ordered a new trial in 1991, citing judicial misconduct. The retrial was delayed because of a series of appeals and motions.
