Any areas of a raster layer which are set to transparent, such as NODATA values, will be black in any VRML exported from ArcScene.
There is a limitation in the way VRML handles transparency: the transparency of the material (the percentage of transparency of the layer) cannot be combined with the transparency of the texture (picture fill symbol or raster). For rasters, the layer's transparency is chosen, since this is used frequently to superimpose different types of information in 3D. The alpha component in the raster pixel buffer is not chosen.
The only thing you can do is set the transparent sections of the raster to opaque colors so that you can control the resulting VRML file.