The pickups that came with the guitar are stock, which means they were made by the manufacturer, in this case Craftsman. To upgrade, there are several viable options; some of the big boys in pickups are DiMarzio, EMG, Seymour Duncan, Bill Lawrence, HAS Sound and so on. U can go to youtube and search for the sound clips of the different pickups. Depending on the sound u want, there shld be pickups that u will like.
As to ur original enquiry, i wld say that u are right. A crap pickup will still sound ok on a good amp, but not the other way around. Go and experiment around with different combinations of pickups and amps to get ur dream tone.