Prosecutors say 64-year-old Stephen Schneider was drunk last month when he struck a channel marker in Barnegat Bay.
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 two children, a brother and sister ages 7 and 9, were thrown from the boat into the water.
They were taken to a hospital where they were pronounced dead.
The crash occurred at night but police say lights on the marker were working properly.
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