| Name | Manhattan end | New Jersey end | Operated | Notes |
| Royal Blue Line Ferry. | South Ferry | Communipaw Terminal | | The Royal Blue was a Baltimore and Ohio Railroad train to Washington, D.C. via Central Railroad of New Jersey and Reading Railroad |
| Communipaw Ferry | Liberty Street Ferry Terminal | Communipaw Terminal | | Central Railroad of New Jersey |
| Jersey City Ferry | Cortland Street Ferry Depot | Paulus Hook, later named Exchange Place, [Jersey City|Exchange Place] | | Pennsylvania Railroad, later via its Jersey City Branch |
| West Shore Ferry | Cortland Street Ferry Depot | Weehawken Terminal | | West Shore Railroad |
| Vesey Street | Hoboken | | Ferry service restored at Battery Park City Ferry Terminal |
| Hoboken Ferry | Barclay Street | Hoboken Terminal | | Delaware, Lackawanna and Western Railroad, later Erie Lackawanna Railway. Originally operated by the Hoboken Ferry Company |
| Murray Street | Hoboken | | |
| Pavonia Ferry | Chambers Street Ferry Terminal | Pavonia Terminal | | Erie Railroad purchased several ferries from previous operators in 1856. Unclear when ferry service from Chambers Street began. |
| Duane Street | Paulus Hook | | Paterson and Hudson River Railroad |
| Franklin Street Ferry | Franklin Street | Weehawken | | West Shore Railroad |
| Hubert Street | Hoboken | | |
| Desbrosses Street Ferry | Desbrosses Street | Exchange Place | 1862–1930 | Pennsylvania Railroad |
| Desbrosses Street | Weehawken Terminal | | West Shore Railroad |
| Spring Street | Hoboken | | |
| Spring Street Ferry | Spring Street | Fort Lee | | |
| Clarkson Street | Communipaw Terminal | | CNJ |
| Christopher Street Ferry. | Christopher Street | Hoboken Terminal | 1838–1955 | Delaware, Lackawanna and Western Railroad. Originally operated by the Hoboken Ferry Company. |
| 13th Street | Bay Street, Jersey City | | Pennsylvania Railroad |
| 13th Street | Weehawken Terminal | | West Shore Railroad |
| 14th Street | Hoboken Terminal | | Delaware, Lackawanna and Western Railroad |
| Hoboken Ferry | 14th Street | 14th Street (Hoboken) | | |
| 23rd Street | Communipaw Terminal | | Central Railroad of New Jersey |
| 23rd Street Ferry | 23rd Street | Exchange Place | | Pennsylvania Railroad |
| Pavonia Ferry | 23rd Street | Pavonia Terminal | | Erie |
| 23rd Street | Hoboken Terminal | | Delaware, Lackawanna and Western Railroad |
| Hoboken Ferry | 23rd Street | 14th Street (Hoboken) | | |
| 23rd Street | Edgewater | | |
| 34th Street | Exchange Place | | Pennsylvania Railroad |
| Weehawken Ferry | 42nd Street | Weehawken Terminal | | West Shore and NYC RR |
| North Weehawken Ferry | 42nd Street | Slough's Meadow | | Weehawken Ferry Company New York Central Railroad |
| 125th Street Ferry | 125th Street | Edgewater | 1903–1941 | Public Service Corporation of New Jersey |
| Fort Lee Ferry | 130th Street | Edgewater | | |
| Englewood Ferry | Dyckman Street | Englewood | 1915–1942 | during colonial era at Closter Dock |