Vertically aligned GaN nanorod arrays with nonpolar InGaN/GaN multi quantum wells (MQW) were grown by MOVPE on c-plane GaN-on-sapphire templates. The chemical and structural properties of single nanorods are optically investigated with a spatial resolution beyond the diffraction limit using tip-enhanced Raman spectroscopy (TERS). This enables the local mapping of variations in the chemical composition, charge distribution, and strain in the MQW region of the nanorods. Nanoscale fluctuations of the In content in the InGaN layer of few percents can be identified and visualized with a lateral resolution below 35 nm. We obtain evidence for the presence of indium clustering and the formation of cubic inclusions in the wurtzite matrix near the QW layers. These results are directly confirmed by high-resolution TEM images, revealing the presence of stacking faults and different polymorphs close to the surface near the MQW region. The combination of TERS and HRTEM demonstrates the potential of this nanoscale near-field imaging technique, establishing TERS as very potent, comprehensive, and non-destructive tool for the characterization and optimization of technologically relevant semiconductor nanostructures.