In order to optimize surface-enhanced Raman scattering (SERS) of noble metal nanostructures for enabling chemical identification of analyte molecules, careful design of nanoparticle structures must be considered. We spatially map the local SERS enhancements across individual micro-aggregates comprised of monodisperse nanoparticles separated by rigid monodisperse 0.9 nm gaps and show the influence of depositing these onto different underlying substrates. Experiments and simulations show that the gaps between neighbouring nanoparticles dominate the SERS enhancement far more than the gaps between nanoparticles and substrate.