Usually when I get pickups rattling, it's the way the pickup's sitting.
I've got two doing it at the moment:
My neck Mule - it's either the springs, or mebbe the braided wire rattling against the pup. If I give it a good wobble it goes away. Next time I have this guitar in pieces I'll be looking into it, mebbe adding more foam under the pickup.
My neck Sultan. Not sure what's doing this at the moment. I suspect the rubber round the screw is too short, so the thing isn't as tight as it could be for the pickup height I'm using at the moment. Not too worried though, these pups are probably moving guitar in the next few months.
My SG develops a loud buzz sometimes as well. Even though I know exactly what it is, it always takes me a few minutes to track it down :roll: - the switch tip comes loose and annoyingly vibrates to A :lol:
Anyway, if it doesn't come through the amp - I tend not to get too worried. I used to use an Epi Les Paul that had awful rattling in the living room. It was the plastic buttons on the tuners, they were all loose. It really annoyed me, but had no effect in rehearsals/gigs so I never bothered fixing it.
Actually (nothing to do with your problem) this last bit reminded me of something about microphonic humbuckers. This is if you're stuck with microphonic feedback in a "no time/money to get them replaced/potted" situation. When I was gigging with that Epi, I found you could tame the squeals by fiddling with the polepieces. Get the thing squealing, then touch each polepiece with the screwdiver. On that Epi, I found that I could usually reduce or stop the squealing by touching one or may two polepieces. I learnt that all I had to do was adjust those slightly (sometimes even just loosen and tighten again to the same setting) and the problem went away for that night.