Authorities said Stephen Schneider was intoxicated when he struck a channel marker in Barnegat Bay last month.
The crash threw two siblings, ages 7 and 9, from the boat. Both children died.
The accident happened the night of July 19, but police said the lights on the channel marker were functioning properly at the time of the crash.
Schneider was charged with two counts of reckless vessel homicide/death by vessel, operating a vessel under the influence, and reckless operation of a vessel, police said.
The investigation remains ongoing.