HE IS NOWHERE on the organizational flow charts in the District Building, but thanks to the homeless-rule traditions of this city and the apprenticeship customs of the U.S. Senate, Alfonse D'Amato of New York has been a powerful "governor" of the District of Columbia for two years. And to the delight of those whom the residents elected to run things in city hall, Sen. D'Amato has been an understanding man of the Senate appropriations subcommittee on the District. Now he is relinquishing this control to take a new Senate assignment, with the city better for his having served.

Two years ago, after Mr. D'Amato defeated Sen. Jacob Javits in the New York Republican primary and went on to win the Senate seat, he was promptly stuck with one of the least-sought chairmanships on the Hill, the D.C. assignment. Immediately, Mayor Barry and others in D.C. government feared the worst: a self-described conservative from Long Island who had campaigned on a strong law-and-order, anti- abortion platform being given financial control over a large, mostly black, mostly Democratic city.

But Sen. D'Amato and his subcommittee turned out to be more supportive of the city on budget matters as well as significant issues of home rule than anyone could have expected. Within a week of taking over the subcommittee, Sen. D'Amato had established a close relationship with Mayor Barry and a deep interest in District affairs. So respectful was he of home rule principles that when anti-abortion groups demanded that no city funds be used to pay for abortions, the senator told them it was up to city officials to make that decision.

This year, Sen. D'Amato was instrumental in winning support for a record $361 million federal payment to the District, plus another $3.1 million to hire more prosecutors in D.C. Superior Court and to buy equipment for the police department.

While we continue to believe that this item-by-item budget control over the District affairs should be eliminated, even if general financial oversight does have to remain with Congress, Sen. D'Amato has earned local thanks for his service. He is leaving, he says, because of a feeling that he was elected to be something other than the "full-time overseer" of this city.

"I've been the defender of home rule," says the senator. "I've spent a lot of time trying to get Congress not to nit-pick everything the District does." His successor as chairman, Republican Sen. Arlen Specter of Pennsylvania, says he, too, believes in "the principles of home rule and that the city should control its own affairs."

That's a good start.