Hydronic heating systems circulate hot water through the radiators. The furnace only fires up when the water cools down, so you could be hearing the circulator pump without hearing the furnace. The fact that you don't hear the noise in the basement makes me suspicious that it's something else. Maybe one of the pipes is a little loose and vibrating against the underside of the floor.
The other possibility is that it's something completely unrelated to the heating system. Phantom noises can be tricky and sometimes it's hard to pinpoint an accurate direction. It could be something electronic....A CFL light, a charger, electric clock, GFI recepticle, etc. One way to narrow that down is to unplug everything in the room......or go to the main breaker box and one-by-one flip breakers until you find which one (if any) stops the noise. That will at least narrow down your search to one circuit, and possibly confirm or eliminate the furnace as the source.