Scott and his girlfriend, Kourtney Kardashian, flew from Los Angeles to attend services for Bonnie late last month, the celebrity news magazine said Thursday.
Bonnie, 63, lived with her husband, Jeff, on Long Island where Scott was raised an only child, E! News said.
E! said Scott has not yet commented on his mom's death.
Scott and Kardashian have been together for seven years and have two children -- a 4-year-old son named Mason and a 1-year-old daughter named Penelope. The couple are cast members of the reality show, "Keeping Up with the Kardashians."