Subway service on the Nos. 1, 2, 3 and 7 has been restored.
The MTA says riders should expect residual delays.
There was no service earlier on the No. 7 between Grand Central Terminal and Queensboro Plaza due to a track fire at the terminal.
The fire department says it responded to a smoke condition there at 9:15 a.m.
Separately, a power failure had knocked out service on the No. 1 and caused limited service on the Nos. 2 and 3 between West 72nd and 125th streets in Manhattan.