Just before 2 p.m. Sunday, police said a car hit the boys while they were walking on the side of the road.
The scouts from Troop 161 were headed for a hike and were with adults when the crash happened.
In all, five boys ranging in age from 12 to 16 were hospitalized.
Rescue workers were forced to administer CPR to one of the victims. Another was airlifted to the trauma center at Stony Brook University Hospital where he is in critical condition.
The other four victims were taken to Peconic Bay Medical Center in Riverhead.
Police arrested 59-year-old Thomas Murphy of Holbrook and charged him for driving while intoxicated.
Murphy is due in court in Central Islip on Oct. 1.
Detectives are asking anyone who may have witnessed this incident to call the Major Case Unit at (631) 852-6555 or anonymously to Crime Stoppers at (800) 220 TIPS.