There is no evidence that an explosion caused a small plane to break apart over Syosset, with scattered debris on the ground suggesting instead that pieces came off “while it was in flight,” a federal investigator said Wednesday.

The pilot and two passengers were killed in the midair accident Tuesday afternoon that caused fragments of the single-engine Beechcraft Bonanza to rain down on a residential neighborhood off Cold Spring Road.

In a distress call to air traffic control minutes before the disaster, the pilot said he was having trouble maintaining control of the 43-year-old aircraft and that more and more of his instruments were malfunctioning, according to National Transportation Safety Board senior investigator Robert Gretz.

The pilot also told the tower the plane’s vacuum pump had broken down, which Gretz said likely would cause some of the plane’s instruments — vital in Tuesday’s cloudy, wet weather — to also fail.

Gretz said investigators have so far recovered the engine and propeller, and identified “the four corners” of the plane — the wings, nose and tail. Smaller pieces must still be retrieved.

The NTSB will also review the plane’s maintenance records, weather conditions at the time of the crash and the pilot’s flight experience. An in-flight breakup is rare, but not unheard of: In 18 years with the agency, Gretz said he’s only investigated five such cases.

One crash victim’s body was found in the parking lot of a BOCES school, another slightly to the west in some woods and the third about 50 yards away in Oyster Bay Cove, Nassau police said. Authorities haven’t publicly identified the victims, pending notification of the families.

advertisement | advertise on newsday

Records show the plane is owned by David C. Berube, 66, of Bristol, Connecticut, who is licensed to fly multi-engine planes and certified to navigate by instruments.

The Hartford Courant identified two of the victims as Berube and his longtime girlfriend, Dana Parenteau. The third victim was a man who worked for Berube, the newspaper said.

“She was a wonderful person,” said a man who answered the phone at the home of Parenteau’s former husband, Edward Parenteau, of Vermont. He declined further comment.

Several of Berube’s family members declined to comment and a call to his Bristol business, New England Municipal Equipment Co., was not returned.

Berube was a stock car racer who began competing in 1990 and competed on the NASCAR Whelen Modified Tour before retiring from the sport in 2013, according to RaceDayCT, a local site that covers racing. Fellow racers exchanged condolences on Facebook.

In a widely circulated post, Ed Flemke, a friend, said Berube was excited to resume racing again when they spoke recently.

“Just had a visit with him last week . . . The usual upbeat smiling guy he always seemed to be!” Flemke wrote.

The plane was more than 3 hours into its flight from Myrtle Beach, South Carolina, to Plainville, Connecticut, when the pilot made his distress call.

“This is kind of a classic accident scenario for a private pilot in instrument flight conditions,” said Robert Mann, president of R.W. Mann & Co., an aviation consulting firm based in Port Washington. The loss of the vacuum system would mean loss of primary instruments and the ability to use autopilot, if one was installed, Mann said.

Without that, the pilot “loses his horizon reference, loses his indication of aircraft orientation,” he said. “So if you then revert to . . . using sensational cues instead of instrument cues, the usual result of that is an over-control situation or a spiral, in which the aircraft quickly builds speed.”

advertisement | advertise on newsday

In trying to slow the plane, the pilot might pull back on the yoke, Mann said, which could lead to an in-flight breakup “because you overstress the primary structure of either wing or the horizontal stabilizer.”

A pilot who loses his instruments “wouldn’t have a sense of right-side up or down,” said Tom Daly, dean of the Dowling College School of Aviation.

Daly said a breakup could result if “the aircraft experienced an extreme high-stress condition which could be the result of over-speed or total loss of control.”

Gretz said he suspects residents will continue to find pieces of debris and the victims’ personal effects for days to come and asked that they call police if that happens.

Out of production since 1985, the Beechcraft Bonanza’s unique feature — its V-tail — was in the late 1980s a source of controversy after it was blamed for in-flight breakups, according to the Aircraft Owners and Pilots Association. Since then, the FAA has issued airworthiness directives requiring tail reinforcements.

advertisement | advertise on newsday

In January, a Beechcraft Bonanza crashed in Colorado after what witnesses described as a midair explosion, according to news reports. The pilot, the sole occupant, died in the crash. The NTSB is investigating the cause.

With Jo Napolitano