Miller was born in Kingston, New York, in 1945 and graduated from Kingston High School and Brown University. He was the news editor of the Gay Community News, the first weekly gay and lesbian newspaper in the United States, from 1975 to 1978, and also served as the paper's features and managing editor. He worked as a staff writer at the Boston Phoenix in the early 1980s.

Miller's most acclaimed book, In Search of Gay America, published in 1989, was the first book to examine gay and lesbian life outside the large metropolitan areas. Miller's subjects include the openly gay mayor of a small Missouri town, gay dairy farmers in Minnesota, a lesbian coal miner in West Virginia, and gay Native Americans in South Dakota. The book won a Lambda Literary Award in 1991 and was honored by the American Library Association. His second book, the ambitious Out in the World (1992), looked at gay and lesbian life in twelve countries around the world, including South Africa, Egypt, Thailand, Japan, Australia, and Denmark. His next book, Out of the Past, was an international survey of LGBT history beginning in 1869, the first time the word "homosexuality" appeared in print. First published in 1995, the book ranged in scope from the story of Plains Indians to the Nazi persecution of homosexuals to America in the age of AIDS. A revised, updated version appeared in 2006.

His interest in gay history led him to write Sex-Crime Panic, an investigative account of the round-up and incarceration of 20 gay men in Sioux City, Iowa, during the McCarthy period. The round-up followed the brutal, unsolved murders of two small children. Although the men were never linked to the crimes in any way, they were labeled as "sexual psychopaths" and incarcerated in a locked ward of a state mental hospital until they were deemed "cured." Sex-Crime Panic received a Lambda Literary Award in 2002, as well as the Randy Shilts Award for Gay Nonfiction from the Publishing Triangle. The story was almost completely unknown until Miller discovered it, tracking down participants and victims in detective-like fashion.

In a departure, Miller's most recent book, Kartchner Caverns (2008) is a nonfiction account of the discovery of stunning limestone caves in southern Arizona by two young men in 1974, and their 25 year quest to save them from environmental degradation. The caves are now an Arizona state park. Kartchner Caverns was the winner of the 2009 Arizona Book Award for "best book," awarded by the Arizona Publishing Association. It also received a Southwest Book Award for 2008 from the Border Regional Library Association. Miller's freelance articles have appeared in the Boston Globe Magazine, the Los Angeles Times, the Cleveland Plain-Dealer, CommonWealth Magazine, the Unitarian Universalist World, The Advocate, and Out. He teaches journalism and nonfiction writing at Tufts University in Medford, Massachusetts.