President Reagan yesterday named T. Allan McArtor, a former Air Force Thunderbirds pilot and now an executive with Federal Express, to head the Federal Aviation Administration.

If confirmed by the Senate, McArtor, 44, senior vice president of telecommunications for the air cargo firm, will succeed Donald D. Engen, 62, who is retiring July 2 after three years as FAA administrator.

McArtor was unavailable for comment yesterday. He would come to the agency at a time when it is under attack almost daily from critics who charge that it is not doing enough to maintain air safety during the peak summer season.

Earlier this week, the Transportation Department announced plans to hire an additional 955 air traffic controllers and supervisors next year to handle a 5 percent increase in traffic.

The announcement followed a six-week dialogue -- public and often sharp -- between the National Transportation Safety Board (NTSB) and the FAA over aviation safety.

The NTSB, warning that air safety is eroding, recommended that the FAA reduce the number of commercial flights this summer. The FAA responded that the skies are safer than ever.

As McArtor's nomination was announced yesterday, Sen. Frank R. Lautenberg (D-N.J.), chairman of the Senate Appropriations transportation subcommittee and one of the FAA's most vocal critics, warned that McArtor would inherit a "legacy of mismanagement and short-sighted policies" at an agency whose credibility, he said, "is on the line."

"I look forward to working with Mr. McArtor," Lautenberg said.

No date has been set for confirmation hearings.

McArtor's appointment has been rumored for weeks, but he is largely unknown in Washington aviation circles.

He has been described by colleagues as "low-key, not inclined to shoot from the hip." McArtor reportedly plays golf, skis and plays tennis in his spare time. His wife, Grace, has said McArtor had a boyhood dream of becoming an astronaut.

McArtor was chosen by Transportation Secretary Elizabeth Hanford Dole after working closely with her as chairman of an advisory committee on the commercial uses of space, one of Dole's pet projects. He was appointed by Dole to the committee in September 1984 and became chairman last August.

At Federal Express, McArtor helped develop ZapMail service, which was abandoned last year after losing almost $300 million.

A 1964 graduate of the U.S. Air Force Academy, McArtor was a fighter pilot for 10 years and was decorated for heroism in Vietnam. In 1971, he obtained a master's degree in engineering from Arizona State University.

Between 1972 and 1974, he was a pilot with the Thunderbirds, the Air Force precision flying team, sometimes working as narrator on the ground.

He joined Federal Express in 1979 and resides in Memphis, where the company has its headquarters. In recent weeks, McArtor has worked out of an office at the Transportation Department preparing for his new job.

Engen announced his resignation in February, saying that he wanted to return to private business. He gave no other reason, but aviation sources said Engen, a retired Navy admiral and former member of the NTSB, had grown increasingly frustrated because he has never been given a free hand by the Transportation Department.

A Senate confirmation vote on McArtor is not expected before Engen departs, which would leave the agency without a chief at the height of the summer travel season. Sources said Engen had been asked to stay on longer but declined.