Niggle (to cause slight but persistent annoyance) appears in the late sixteenth century, with unknown though likely Nordic origin, and shares no etymological relation to the infamous racial slur. It is, like niggard, a benign word. However, it also bears an uncomfortable lexical proximity to a contemporary slur for black children, so I must caution its use: know your setting and your audience. Some (not the educated sort) may be unforgiving even when presented with the words’ etymological and lexical innocence.