Contract workers should be paid for the holiday, Foye wrote, as are Port Authority and airline employees, and the pay should apply retroactively to the holiday this month.
(Read more: Minimum wage protests raise awareness, but not pay)
"Employees of your contractors should enjoy the same benefit, especially in light of the importance of this holiday to our country's history and values," he wrote.
The letter was sent the same day that President Obama announced in the State of the Union address that he was signing an executive order raising the minimum wage for future federal contract workers to $10.10 an hour. The Daily News first reported on the letter Wednesday.
The campaign by S.E.I.U. Local 32BJ, a union representing building services employees, has gone on for more than a year and has drawn attention to the more than 12,000 people who work for contractors hired by airlines and terminal operators at New York-area airports. Some of the workers, who clean the cabins of planes, move baggage or push wheelchairs inside the terminals, make less than $8 an hour.
(Read more: Debating the effects of a $15 fast food wage)
Last week, 32 people were arrested outside La Guardia Airport at a march led by the union on Martin Luther King's Birthday. Some local politicians were arrested, including Rep. Charles Rangel (D-N.Y.) and several City Council members.
The letter from Foye, who was appointed by Gov. Andrew Cuomo of New York, also said the Port Authority wanted to work with the airlines and the union to improve wages and benefits for all airport workers over the next three to five years.
The union said it was pleased that the protest last week seemed to have made a difference.
(Read more: Airport upgrades: Changing rooms, outdoor plazas)
"Pat Foye's letter is a promising step forward," the union's president, Hector Figueroa, said, "and marks the first real progress we have made in lifting thousands of contracted airport workers out of poverty."