Cutbacks had left just one unit patrolling in the morning and early afternoon.
A 28-foot boat breached the restricted waterway around LaGuardia Saturday and crashed into a pier. The boat captain is charged in that crash with navigating a vessel while intoxicated.
The authority will assign a boat, manned by two officers, to each airport from 2 p.m. until 10 p.m., known as the second platoon.
The patrols will resume Thursday.
That shift was altered after last summer, leaving a unit patrolling only between 6 a.m. and 2 p.m.
The crash technically occurred during the 10 p.m. to 6 a.m. third platoon, which will still not be staffed by Port Authority boats. However, there is little aviation traffic during that time.