They probably meant "throw-out" bearing (which rides on the pressure plate fingers when you depress your clutch pedal). The input shaft bearing is inside the trans.
I also doubt that VIP will cover clutch parts as they're considered to be wear items, like brake pads and rotors.

To get a dealership (or otherwise) tech to hear what you're hearing, request to go on a test drive with the technician (an EXPERIENCED technician, not a rooky). When you're driving the car with him and you hear the noise, you then say "that noise" and then no one can say that they didn't hear anything.

Being a tech, you'ld be surprized how often when I go on test drives with customers the noise doesn't occur and they'll say "it was doing it all the way here" or "all day yesterday".....I'd say about 90% of the time too (more often than not). If you can't duplicate the noise, no one will want to guess at parts w/o hearing it as it's too easy to guess wrong.