Six reputed members of the Bonanno crime family were indicted yesterday in an alleged racketeering conspiracy involving three murders, gambling and drug peddling. Two also were charged with an attempted armed robbery at the home of the sister of the late shah of Iran.

Lee F. Laster, assistant director of the FBI's New York office, said the indictments and arrests "deal a very serious blow to the Bonanno family." The charges stem from a five-year undercover inquiry that Laster said was "one of the most extensive and long-running in memory."

Charged with conspiracy by a federal grand jury in Manhattan were Dominick (Sonny Black) Napolitano, a reputed captain in the Bonanno family, and five alleged underlings: Benjamin (Lefty) Ruggiero; John (Boobie) Cerasani; Nicholas (Nicky) Santora; Antonio (Boots) Tomasulo, and James (Jimmy Legs) Episcopia, 43. Napolitano, Ruggiero, Cerasani and Santora also were charged with racketeering in a separate count.

Santora, Tomasulo and Episcopia were arrested. Cerasani was expected to surrender. A Dec. 3 arraignment was scheduled.

Napolitano has been at large since being named earlier this year in a federal court complaint that alleged he and Ruggiero were involved in the slayings of three rivals in the Brooklyn-based Bonanno family. Ruggiero has been in custody since Aug. 31 on the complaint.

In addition to Napolitano and Ruggiero, the indictment accuses Santora in the murders of Alphonse (Sonny Red) Indelicato, Philip Giacone and Dominick Trinchera, the three rival leaders.

Napolitano and Cerasani were accused of attempting to rob the occupants of a house belonging to the sister of the late shah, and they were accused along with Santora with distributing methaqualone, a depressant, and with operating an illegal gambling business.

In Oakland, Calif., meanwhile, the son of Joseph (Joe Bananas) Bonanno, reputedly the former head of the New York crime family, was behind bars after 10 months as a fugitive. Salvatore (Bill) Bonanno, who is being held on charges of bilking the elderly in a home remodeling fraud, was arrested by Mexican police at resort south of Tijuana and turned over to the FBI at the border.

Bonanno disappeared after his indictment Jan. 15 along with his brother, Joe Bonanno Jr., and two others on 22 counts involving Bonanno-owned construction companies.