This is from the realdeal forum:

Bonanno Members Who Have Died Since 1998:
Nicholas Accardi (2002)
John “Big Head” Arcaro (2001)
Giuseppe Arcuri (2001)
Joseph Benanti (2007)
Anthony Bonacci (2001)
Joseph “Joe Bananas” Bonanno (2002)
Salvatore “Bill” Bonanno (2007)
Salvatore Bruno (2006)
Gaspar Cammarata (Died 1999)
John “Boobie” Cerasani (2007)
Joseph “Junior” Chilli (2008)
Salvatore "Paintglass" D’Ottavio (1999)
Alfred "Al Walker" Embarrato (2001)
John “Johnny Green Eyes” Faraci (2011)
Salvatore “Sally Fruits” Farrugia (2007)
Anthony Lucido (2010)
Nicholas "Nicky Cigars/Glasses" Marangello (2000)
Louis “Louie Cigars” Mele (2007)
Gerlando “Georgie from Canada” Sciascia (1999) (Killed)
Salvatore “Sally Bross” Scudiero (2006)
Anthony "Little Anthony" Seccafico (2009) (Killed)
Anthony Spero (2008)
Joseph “Joe T” Taoromina (2001)

Additional names to the Bonannolist:
Vincent "Jimmy; Fort Lee" Capasso (1999)
Frank Cotroni (former member) (2004)
Anthony Ditri (later transfered to San Jose, California) (2005)
Johnny Ligamari (suspected member) (1999) (suicide)
Salvatore "Sal; the Ironworker" Montagna (deported to Canada) (2011) (killed)
Frank "Cheech" Navarra (2000)
Nick Rizzuto (former member) (2010) (Killed)


Gambino Members Who Died Since 1998:
Anthony Accardi (1999)
James Andorlini (2009)
Joseph "Joe" Arcuri (2007)
Louis "Louie Fats" Astuto (1999)
Anthony “Todo” Anastasio (2010) (Suicide)
Salvatore "Toddo" Aurello (1998)
Robert "Bobby Cabert" Bisaccia (2008)
Lawrence Bonomo (2008)
Michael Bove (2001)
Liborio “Bobby Red” Crapanzano (2001)
Dominick Castore (2003)
Michael Catalano (1998)
Joseph "Joe Butch" Corrao (2001)
Samuel "Little Sammy" Corsaro (2002)
Frank "Frankie Dap" D'Apolito (1998)
John Daniello
Louis DeFillippo
John DeMatteo (2006)
Gregory "Greg" DePalma (2009)
Jerome DeQuillo
Paul DiBella (2005)
James "Jimmy Brown" Failla (1999)
Daniel “Danny Wagons” Fatico (2006)
Joseph Gambino (2004)
Joseph Giardina Jr. (2002)
John "Handsome Jack" Giordano (2009)
Joseph Giordano (2005)
John “Johnny Boy” Gotti (2002)
Frank "Frankie Butch" Guglielmini (2010)
David “Davie Crockett” Iacovetti (1998)
Frank Insernia
Joseph “Joe the Cat” LaForte Sr. (2001)
Pasquale Lauro
Philip “Phil/The Hammer” LoScalzo (2001)
Joseph “JoJo” Manfredi (2002)
Samuel “Sam” Mannino (2004)
Joseph “Joe/Peanuts” Messina (1999)
Ralph “Ralphie Bones” Mosca (1999)
Charles “Buddy Musk” Muccigrosso (2010)
Vincent Palmisano (1999)
Anthony “Guido” Penosi (2010)
Peter “Petey 17” Piacenti (2007)
Anthony Pimpinella (1999)
George "Fat George" Remini (2007)
Victor Riccitelli (2009)
Natale "Big Chris" Richichi (2001)
Anthony “Fat Andy” Ruggiano (1999)
Frank “Little Frank” Ruggiero (2002)
John “Johnny Boy” Ruggiero (2008)
Nunzio Russo (2002)
Louis Salica (2002)
John Santoro Sr.
Vincent Sarullo (2002)
Salvatore "Fat Sally/Uncle Sal" Scala (2008)
Angelo Scarpulla (2008)
John Sciascia (1998)
Anthony “Tony Pep” Trentacosta
Paul "Paulie Zac" Zaccaria (2007)

Additional names to Gambino list:
Joseph Bove (1998)
Anthony Carminati (1998)
Joseph "Gus" Colozzo (1999)
Pasquale "Patsy" Conte (2000)
Pasquale Crapanzano (1998)
Joseph Giardina Sr (2001)
Anthony "Tony Naps" Napolitano (2000)
Louis Rumore (2001)


Colombo Members Who Have Died Since 1998:
Anthony "Abbie Shots/Shatz”" Abbattemarco (2005)
Benedetto "Benny" Aloi (2011)
Robert Barbieri (2002)
Peter Campisi (2002)
William "Wild Bill" Cutolo (1999) (Killed)
Jerome D’Agati (2001)
Paul Damico (2002)
Leonard Dello (2009)
Robert Falvo (2010)
Joseph “Joe Black” Gorgone (2010)
Ernest LaPonzina (2004)
Benjamin Locicero (2003)
Albert Maione (2003)
Louis "Bo Bo" Malpeso Sr. (2003)
Ralph Piccirillo (2001)
Philip Rossillo (1998)
Joseph "Joey Flowers" Rotunno (2005)
Joseph "JoJo" Russo (2007)
Joseph Sangiorgio (2001)
Anthony “Scappy” Scarpati (2002)
Anthony Scianna (2009)
Joseph "Joe Yack" Yacovelli (2006)

Additional names to the Colombo list:
Frankie "the Beast" Falanga (suspected member) (2003)
Joseph Juliano Sr (2002) (likely)


Genovese Members who Have Died Since 1998:
Vincent “Jimmy Blue Eyes” Alo (2001)
John "Buster" Ardito (2007)
Adolfo "Big Al" Bruno (2003) (Killed)
Nicholas Bufania (1998)
Philip Buono (2006)
Frank Camiscioli (2000)
Gerardo “Jerry” Catena (2000)
Frank Catenacci (2011)
Frank “Frankie California” Condo
Ralph Conte (2002)
Ralph Coppola (1998) (Killed)
Thomas “Pee Wee” DePhilips
Emilio "The Count" Delio (1998)
Anthony Delevo (2006)
Charles “Chuck Tourine” Delmonico (2008)
Vincent “Vinny” DiNapoli (2005)
Albert “Chicky” Facciano (2011)
Edward Falco (2003)
Sabato Falgiano (2000)
Mario "Choda" Fiore (2005)
Tino "The Greek" Fiumara (2010)
Joseph “Joe Glitz” Galizia
Joseph "The Eagle" Gatto (2010)
Louis “Straky/Lou Red” Gatto (2002)
Enrico “Red Hot” Gentile (2003)
Joseph Gerardo (2002)
Anthony Giacalone (2011)
Vincent "The Chin" Gigante (2005)
Carmine “Buddy” Gualtiere (2005)
Rudolf “Ruddy Cue Ball” Izzi (2007) (Killed)
Nicholas “Nicky Shuffles” LaGuardia (2003)
Anthony “Pee Wee” Lanza
Salvatore "Sally Dogs" Lombardi (2009)
Anthony “Tony L” Lucania (2009)
Leonard “Lenny” Macaluso (2003)
Nino Maccioli (2011)
Joseph Maida (2002)
Sam Felippo Manarite (2006)
Vincent Martino (2002)
Carlo Mastrototaro (2009)
Aldo Mazzarati (2004)
Alexander “Black Alex” Morelli (2003)
Mario Mosiello (2001)
Louis Moscatiello (2009)
Salvatore Napurano (1998)
Vincent Pacelli (2002)
Rosario Palmieri (2007)
Carmine Pellegrino (2003)
Michael “Mike” Perrone (1999)
Rocco Perrotta (2005)
Thomas “Tommy” Principe (2000)
Lawrence Ricci (2005) (Killed)
Joseph Ruggiero (2006)
Joseph “PePe” Sabato (1999)
Anthony “Turk” Scibelli (1998)
Francisco "Frank Skyball" Scibelli (2000)
Frank "Farby" Serpico (2002)
Ralph Serpico (2001)
Joseph Schipani (2003)
Joseph “Joe Stretch” Stracci
“Big Funzi” Tarricone (1999)
Joseph Tedeschi (1998)
John Verra (2007)
Frank Vispisiano (2011)
Nicholas Vitulli (2006)
Joseph “Joe Z” Zarra

Additional names to Genovese list:
Albert "Big Larry" Landi (2002)
Ciro Perrone (2011)
Joseph "Hoboken Joe" Stassi (2002)
Anthony Volpe (2010)


Lucchese Members Who Have Died Since 1998:
Victor Aita (2005)
Frank "Frankie Hearts" Bellino (2001)
Nicholas Bonina (2002)
Frank Borelli (2005)
Charles Carlino (2002)
Samuel Castaldi (1998)
Salvatore Ciccone (1999)
Albert Circelli (2003) (Killed/Not Mob Related)
Antonio "Tony Ducks" Corallo (2000)
Ralph “Raffie” Cuomo (2008)
Charles DiPalermo (2009)
Ciro 'Charley Baker' Giampaolo (2000)
Michael LaBrabera Sr. (2007)
Michael "Big Mike" LaBarbera Jr. (2004)
Frank Lagano (2006) (Rat,Killed)
Daniel Latella (2003)
Nicholas Lessa (2001)
Andrew Licari (1999)
Richard “The Toupee” Pagliarulo (1999)
Victor Panica (2005)
Antonio Pinto (2004)
Salvatore "Tom Mix" Santoro (2000)
Anthony “Torty” Tortorello (2000)
Charles Tuso (2003)
Angelo Urgitano (1998)

Additional names to Lucchese list:
Joseph "Chick" Foti (2004)
Saverio "Sibby" Maimone (2003)
Frank J. Nuccio (2005)
Anthony Porcelli (2009)
Joseph Ragone (2000)
Angelo Tacetta (2002) (likely)