The injured were rushed to University of California, San Diego Hospital, where the boy was declared dead, Luque said.
Five others were treated for serious injuries.
"They're all considered major traumas," Luque said.
No names or details of the injuries were released.
Neither boat was participating in the parade, said Ron Sheehan, spokesman for the San Diego Bay Parade of Lights, in which more than 80 vessels festooned with Christmas lights and decorations cruise through the bay.
Many boats full of spectators filled the bay to watch the parade and fireworks. But the Coast Guard did not say if the recreational boat was among them or how close the accident occurred to the parade area.
Authorities have not said how the accident occurred, but it came just after sundown in clear weather with light winds.
Sandy Fenten told the San Diego Union-Tribune she was sitting on Harbor Island when she saw a boat with emergency lights head toward downtown San Diego, then turn around and collide with another boat.
"All of a sudden, you heard this tremendous thud or crash," said Fenten.
The parade's Web site said an estimated 80,000 people were expected to attend the last of eight nights of the parade Sunday, which also featured a fireworks show.
The 87-foot Coast Guard cutter Haddock had been scheduled to lead the parade, which was supposed to begin about the same time as the accident, but was called away to the collision scene.
The parade otherwise continued as planned, Sheehan said.
Paramedics took the child victim to a fuel dock at Harbor Island then taken by ambulance to the hospital, and the five injured adults were taken by boat to Shelter Island, then by ambulance to the hospital.
The Coast Guard patrol boat was responding to a report of a grounded vessel at the time of the collision, spokeswoman Jetta Disco said.
The cause of the crash was under investigation, she said. It was not clear how fast either boat was traveling.
Both boats returned to shore and were being assessed for damages, Disco said. The size and type of civilian boat were not released.
San Diego Harbor Police and the San Diego Fire Department assisted in the rescue efforts, said Coast Guard Lt. Josh Nelson.