Hunter took the puck in the slot and beat Antero Nittymaki for his 19th goal as the Islanders moved into a tie for seventh place in the Eastern Conference with Montreal.
Jason Blake, who the team had considered dealing at the deadline, had three goals and an assist for the Islanders, and Chris Simon also scored. Rick DiPietro stopped 29 shots as New York improved to 5-1-0 on its seven-game home stand.
The Flyers, who twice rallied from three-goal deficits, were led by R.J. Umberger's two goals. Sami Kapanen, Dimitry Afanasenkov and Simon Gagne had the others while Nittymaki stopped 33 shots.