The NY lodging houses have been featured in a number of fictional works over the years. In chronological order, these include...
Horatio Alger, Jr.'s stories.
Alger (1832-1899) is best known for the great number of books he wrote featuring street boys and their rise from poverty to success via hard work, integrity, and kind benefactors. Some stories, such as Mark the Match Boy and Ragged Dick, feature the earlier LH at Fulton St.; Rough and Ready is possibly set at the Park Place LH; others set later, such as Cast Upon the Breakers, have scenes at the DSLH (during its early years, when O'Connor was still Superintendent). Alger himself was invited by Brace to stay at the DSLH, and the author had a reserved bed and desk there for several years, researching his stories.
See also: Horatio Alger, Jr. Resources (thanks to the site's owner for permission to link).
Never Give Up; or, The News-Boys.
A novel published by Madeline Leslie in 1864. The book is dedicated to the CAS specifically for their work with the Newsboys' LH, and the story itself features a fictional LH based closely on the real one (which at the time would have been the Fulton St. LH).
"The Kid Hangs Up His Stocking."
Christmas short story by Jacob A. Riis, printed in the Nov. 1899 issue of The Century. It is set in the West Side LH.
Edward W. Townsend's stories.
Townsend's series of stories about Bowery boy Chimmie Fadden were inspired by a visit to the DSLH (a reporter for the Sun, he had been sent to cover a newsboys' dinner). The stories were published in the mid-1890s in both the Sun and in book form, and were hugely popular at the time.
1938 film starring Jackie Cooper as a newsboy who throws his loyalty behind one of two warring papers. According to the plot keywords on IMDB, it apparently is set in New York, possibly in the Lower East Side.
This 1992 movie musical released by Disney and directed by Kenny Ortega centers on a ficionalized account of the 1899 Newsboys' Strike. It stars a large cast headed by Christian Bale, David Moscow, Robert Duvall, Ann Margaret, and Bill Pullman. One of Disney's biggest live-action flops at the box office at the time of its release, the movie eventually gained popularity and even cult status on home video. The opening scenes of the movie take place at the DSLH.
The strike as depicted in the movie, in which the boys strike because of a rate hike from 50 to 60 cents per hundred in 1899, is a conflation of two real-life newsboy strikes against the New York World and New York Journal. (It should also be noted that newsboy strikes were, though not common, not new either: by this time they had been occurring for years in New York and elsewhere in the US.) The first of these began May 9, 1898, when both World and Journal raised the price of papers sold to newsboys from 50 cents per hundred to 60 cents per hundred. It lasted until at least May 16 and gained the support of some other worker's unions along the way, such as the union of metal polishers, which agreed not to buy those two papers. The issue was raised at the May 15 meeting of the Central Labor Union, which declined to take up the matter because it was "too small." The second and larger strike occurred over a year later, beginning July 20, 1899, again against those two papers. There are at least two different accounts of the cause: An article in the Brooklyn Eagle later that day stated that the reasons were due to the prices being raised to 70 cents per hundred, but articles from the New York Times in following days explained that it was because the prices, having been raised in 1898 (the prompt for the first strike) at the onset of the Spanish-American War, had not gone back down despite the War's end.
The Newsboys' Lodging House or, The Confessions of William James.
2004 novel by Jon Boorstin. I have not read this book yet, but as far as I know it's set in 1872, which would presumably set it in the Park Place Lodging House.