Currently the geojson tools only support writing json with 2d coordinates. It does support reading both 2d and 3d coordinates.
The following code snippet shows the problem. Of writing a 3d point.
GeometryJSON geoJson = new GeometryJSON();
GeometryFactory factory = new GeometryFactory();
Point point = factory.createPoint(new Coordinate(10,11,12));
String json = geoJson.toString(point);
Point p = (Point)geoJson.read(json);
WKTWriter writer = new WKTWriter(3);
String jp = writer.write(p);
A simple patch is required to the CoordinateSequenceEncoder inside the GeometryJSON class. I have attached a patch that is working for me.