- Seganus Thatch
- Seifert Corners
- Selden
- Selkirk
- Selkirk
- Semans Corner
- Sempronius
- Seneca Castle
- Seneca Falls
- Seneca Heights
- Seneca Hill
- Seneca Knolls
- Seneca Manor Mobile Home Park
- Seneca Mills
- Sennett
- Sentinel Heights
- September Place Mobile Home Park
- Setauket
- Setauket-East Setauket
- Seth Green Island
- Seven Isles
- Seventh Day Hollow
- Severance
- Severance
- Sevey
- Sewalls Island
- Seward
- Sexton Island
- Shackport
- Shad Island