The NYPD had information that a man involved in a weekend shooting in Harlem had fled to New Bedford, and was staying with a woman at the Bay Village Housing Development.   When members of New York's Violent Fugitive Squad joined New Bedford officers this morning in a search of the Acushnet Ave apartment, they found 44-year-old Jose Cintron hiding under a bed.   Police found 120 grams of heroin and two rounds of ammunition in his possession.   Cintron has been charged with trafficking heroin, trafficking heroin within 100 feet of a playground, unlawful possession of ammunition and being a fugitive from justice.   The victim of the New York shooting is expected to survive.