We use the suite of Milky Way-like galaxies in the Auriga simulations to determine the contribution to annihilation radiation from dark matter subhalos in three velocity-dependent dark matter annihilation models: Sommerfeld, p-wave, and d-wave models. We compare these to the corresponding distribution in the velocity-independent s-wave annihilation model. For both the hydrodynamical and dark-matter-only simulations, only in the case of the Sommerfeld-enhanced annihilation does the total annihilation flux from subhalos exceed the total annihilation flux from the smooth halo component within the virial radius of the halo. Progressing from Sommerfeld to the s, p, and d-wave models, the contribution from the smooth component of the halo becomes more dominant, implying that for the p-wave and d-wave models the smooth component is by far the dominant contribution to the radiation. Comparing to the Galactic center excess observed by Fermi-LAT, for all simulated halos the emission is dominated by the smooth halo contribution. However, it is possible that for Sommerfeld models, extrapolation down to mass scales below the current resolution limit of the simulation would imply a non-negligible contribution to the gamma-ray emission from the Galactic Center region.