| Albany–Rensselaer Station (ALB) |
| Amsterdam Station (New York) (AMS) |
| Buffalo–Depew Station (BUF) |
| Buffalo–Exchange Street Station (BFX) |
| Croton–Harmon Station (CRT) |
| Fort Edward Station (FED) |
| Hudson Station (New York) (HUD) |
| Louise M. Slaughter Rochester Station (ROC) |
| New Rochelle Station (NRO) |
| New York State Fair Station (NYF) Seasonal stop |
| Niagara Falls Station (New York) (NFL) |
| Penn Station (New York City) (NYP) |
| Plattsburgh Station (PLB) |
| Port Henry Station (POH) |
| Port Kent Station (PRK) Seasonal stop |
| Poughkeepsie Station (POU) |
| Rhinecliff–Kingston Station (RHI) |
| Rome Station (New York) (ROM) |
| Rouses Point Station (RSP) |
| Saratoga Springs Station (SAR) |
| Schenectady Station (SDY) |
| Ticonderoga Station (FTC) |
| Union Station (Utica, New York) (UCA) |
| Westport Station (New York) (WSP) |
| Whitehall Station (WHL) |
| William F. Walsh Regional Transportation Center (Syracuse) (SYR) |
| Yonkers Station (YNY) |
