Your best bet is really to grab the fastest lens you can: light-collecting ability is far more important than high ISOs, if you want to manage to get good quality low-light lenses. I think that a D90 plus an f/1.4 50mm would probably serve fairly well. Is there a reason you have to go with only a camera, not a new lens?
a 50mm f/1.8 is a good MUCH cheaper option than a new boddy.
But if you were to go with one of the bodies you mentioned, Id go with the D60, or even better the d40. (Same camera, faster flash sync, which is something youd want to use in low light, just with a few less pixels and its cheaper)
You might want to go with the D90 for low light performance.