Next step: The next time you hear the noise at night, go check to see if the water heater is on (burner going). If it is, turn the gas off (so the burner shuts down) and go check to see if the noise goes away. If the noise is still there, go back to the water heater and release the T&P valve to relieve any built up pressure in the water heater. Go check for the noise again.
These are just some next steps to check as you eliminate causes.
Have you thought about wind over the flue? Is the wind blowing when you hear the noise?
You will hear the noise louder at night because the background noise level is less.
[Edited by Jerry Peck on 13 October 2000]