This Red Hook Water Polution Control Sewer Map from 1975 shows the existing sewers at that time. 

The map shows four sewer lines ending in Atlantic Basin.   Pipes discharging into the harbor, or other bodies of water, are known as Combined Sewer Overflows, or CSOs for short.   Sewer lines are connected to street drains. During heavy rains, for example, the system gets more water than it can handle and the overflow goes - untreated - right into the harbor.  Click here, or below to see the full  1975 map. 

The New York City Department of Environmental Protection also has a Municipal Separate Storm Sewer System Map.  (They call it a MS4 Area Map).
The DEP website says that their map is for informational purposes only and that:
"New York City’s MS4 Stormwater Management Program is a multiagency effort led by the Department of Environmental Protection (DEP) to reduce pollution in stormwater runoff in the MS4 Area of NYC. This MS4 Map represents the known MS4 outfalls and drainage areas as of August 1, 2020 and provides additional data relevant to the MS4 Permit. The MS4 Map only shows areas draining to the Municipal Separate Storm Sewer System. DEP also maintains combined sewer and sanitary sewer systems; these service area delineations are not represented on this map. 

Open Sewer Atlas NYC, provides a similar map of the sewershed. 

New York State provides a digital map of Combined Overflows.   The map is embedded below.  Zoom into Red Hook to see the outflows there.