It's going to depend on the sensitivity of your microphone and the strength (or weakness) and susceptibility to overload of the preamp in your unit.
With my minidisc, there was no choice: the preamp overloaded with even a modest amount of bass, so it was line-in or#$(&#%. With my PCM-M10, and a fairly new pair of lower-sensitivity mics, I can get away with a lot louder music via mic-in (low-sensitivity). But if I think it's going to be LOUD then it's battery box-line-in time.
Line-in and battery box should also provide a cleaner signal because there is noise from every preamp, but when loud music is being recorded, that's not really a factor.