Boston College quarterback Doug Flutie, winner of this year's Heisman Trophy, was welcomed by President Reagan yesterday as "a young man who stands in a class by himself." During a brief ceremony in the Executive Office Building, Reagan was introduced to Flutie's family and received a miniature of the trophy awarded annually by New York's Downtown Athletic Club to the outstanding college football player of the year.

After accepting Reagan's congratulations, Flutie turned to members of the Gonzaga High School team, who had been invited to attend the ceremony, and told them, "If you could dream it, it's possible." . . .

Howard Schnellenberger will collect $140,000 a year under his five-year contract as football coach at Louisville, with $250,000, plus interest, in deferred compensation to be paid at the end of the period. Louisville President Donald Swain explained the agreement to the school's faculty senate, adding that Schnellenberger will receive $70,000 a year in regular salary and $70,000 for television appearances . . .

Billy Hunter, former Baltimore Orioles coach and Texas Rangers manager, is the new athletic director at Towson State University, the school announced. Hunter, 56, had been acting a.d. since June 14.