Police say the man asked a clerk at the Deegan Motel in the Jerome Park section to use the bathroom.
He went into the building, took out a gun, tied up the clerk, stole an unknown amount of cash and ran.
The suspect is described as a black man in his 30s, about 5-foot-7 with a thin build, and he carried a red backpack.
Anyone with information is asked to call Crime Stoppers at (800) 577-TIPS (8477).
The public can also submit their tips by logging onto Crime Stoppers' website at NYPDCrimeStoppers.com or by texting their tips to CRIMES (274637), and then entering TIP577.