The last name Naicker occurs in Germany, possibly in the 19th Century. What is the origin, history and meaning of this name?
It would be really helpful to know in what document(s) you've seen the name referenced. It is possible that the name was mis-transcribed or mis-spelled or is native to small locality. Naicker is an odd spelling, and according to various current German resources, does not exist today.
A similar name, Naecker, while rare, is represented in several areas of northern Germany and in Landkreis Sankt Wendel, Saarland [per the Geogen database, based on German telephone records]. That there are 2 widely separated regions of occurrance (and not just larger cities) suggests multiple origins for the surname. The Saarland cluster may be derived from the river Neckar.
There are both general and regionally specific handbooks for German surname meanings (see Literaturhinweise for titles). The general ones often omit very rare names. To use the regional books, one should be sure of the locality and time-frame where the name occurred. Regional resources will describe patterns of name formation and vocabulary that are used locally.
As bgwiehle wrote, it could come from the river Naecker which in turn could be related to the mythologic figure of Necker, Nikker, Nixe, ... present in germanic and scandinavian legends. The Necker is a water spirit. The (West)-Flemish name De Necker's etymology is explained in this way.