The Reagan administration appears to be moving into a new controversy involving the choice of a new head for the St. Lawrence Seaway Development Corp., the federal agency that runs the American portion of the U.S.-Canadian waterway project.

The White House choice is former representative Eugene V. Atkinson of Pennsylvania, who switched from the Democratic to the Republican Party last year and then lost his seat in the November election.

Atkinson is backed by White House chief of staff James A. Baker III, presidential advisers Edwin Meese III and Michael K. Deaver, White House congressional liaison chief Kenneth Duberstein and political aides Edward Rollins and Lee Atwater, according to White House sources.

However, just before he left office, secretary of transportation Drew Lewis, under whose jurisdiction the Seaway falls, recommended to President Reagan that the job go to James L. Emery, the former New York State Assembly minority leader, who lost his race for lieutenant governor last fall.

Lewis had asked New York GOP leaders for a recommendation, and state chairman George Clark, whose pro-Reagan credentials go back to the 1976 national convention, named Emery.

New York GOP congressional leaders, sparked by Sen. Alfonse M. D'Amato, who serves on the Appropriations subcommittee for Seaway operations, and Rep. David O'B. Martin, a member of the House GOP whip organization and in whose district the American seaway operation is headquartered, strongly backed Emery.

The 12 senators from the six upper Great Lakes states, meanwhile, wrote to White House personnel director Helene von Damm urging the reappointment of the present Seaway chief, David W. Oberlin, who has held the job since 1969 and was a port director at Duluth, Minn., and Toledo, Ohio.

Oberlin was named to the first seven-year statutory term for the Seaway job by President Ford, who has written to Reagan recommending Oberlin's retention.

Several Great Lakes groups, including port officials, are supporting Oberlin, whose term expires at midnight tonight. Associate Administrator William H. Kennedy will be acting administrator for 30 days until the new chief is confirmed.

No matter which way the White House goes, it will run into considerable flak on Capitol Hill.

Lewis had decided against reappointing Oberlin and, even though Atkinson is a fellow Pennsylvanian, was backing Emery. When Elizabeth Hanford Dole replaced Lewis as secretary of transportation she committed herself to his choice.

The Pennsylvania congressional delegation has been silent about their former colleague. His appointment has not been pushed by Sens. John Heinz and Arlen Specter, both Republicans.

Some congressional Republicans criticize the proposed Atkinson nomination as a "political payoff" for Atkinson's party switch, but the White House appears to be standing firm.

The letter from the upper Great Lakes senators--six Republicans and six Democrats from Illinois, Ohio, Indiana, Michigan, Minnesota and Wisconsin--praised Oberlin as an "excellent manager" and "an excellent statesman" with the experience necessary to deal with his Canadian counterparts.

The Great Lakes senators say they are suspicious of New York's stand because former governor Hugh L. Carey and his successor, Gov. Mario Cuomo, oppose testing for winter navigation on the St. Lawrence River. Environmentalists contend that breaking the ice would have an adverse effect on wetlands, while lake interests say such navigation is essential to reaching the seaway's potential.

The Great Lakes senators argue that the Midwest is suffering economically and that Oberlin had consistently succeeded in minimizing the Seaway's "inherent disadvantages" as a transportation system.