The city wants to crack down on the longtime practice of illegal boarding houses for the formerly homeless, where for years landlords have been charging down-on-their-luck tenants hundreds of dollars a month for a bunk bed in a run-down house. There are dozens of these kinds of illegal boarding houses, according to the city, concentrated in poor neighborhoods in Brooklyn and the Bronx. Many are overcrowded, with as many as 60 people living in a two-family home. Yesterday, the city took a decisive step in putting an end to these operations by ordering the Department of Homeless Services and staff members in non-profit shelters to stop referring homeless people to buildings that have been cited as unsafe in city inspections. Shelters that break the rules will be issued fines.