The stores are underneath the elevated B subway station on 86th Street in Bensonhurst.
The fire were first reported around 9:45 this morning and quickly went to three alarms.
According to eyewitnesses, the fire raged through two restaurants, an optometrist office, a hair salon, and a beauty school.
The uncontrolled fire proved difficult for the 138 firefighters to bring under control.
16 firefighters were treated for heat exhaustion and other minor injuries.
No one else was hurt in the fire.
The cause is under investigation.