William Diaz, 42, of 10 Margaret St., Glen Cove, was found to have "several plastic bags of crack cocaine," according to a police statement.
The car, a Volkswagen Passat, had a bullet hole in the rear passenger door and another in the front passenger door window, Nassau County police said.
Police said it is unclear if Diaz was involved in the shooting and that an investigation is ongoing.
The victim, 39, apparently was shot on Sterling Place in Hempstead, according to police.
The man, whose identity has not been released, suffered a perforated bowel that required surgery and also had his appendix removed.
Police said the shooting took place at about 10:45 a.m.
Diaz was charged with third-degree and fourth-degree criminal possession of a controlled substance. He is scheduled for arraignment Tuesday in First District Court, Hempstead.
Police are asking anyone with information about the shooting to contact Crime Stoppers at 800-244-TIPS. All calls will remain confidential, police said.