Allen H. Seed Jr., retired executive director of Keep America Beautiful, a national anti-litter organization, died apparently of natural causes in his sleep Thursday at his home in Manhattan. He was 87 years old. Mr. Seed was associated with Keep America Beautiful from the early 1960's to 1972, when he retired. He was also executive vice president of the National Municipal League, a group that advocates good government, from 1950 to 1962. An avid stamp collector, he was a governor of the Royal Philatelic Society. He was a native of Brooklyn. He is survived by his wife, the former Eva Standish Matthews; three sons, Allen H. 3d, of Boston, Dr. William T., of Manhattan, and Peter H., of St. Paul; a daughter, Eva Auchincloss, of San Francisco; 10 grandchildren, and two great-grandchildren.