We investigate how strong lensing of dusty, star-forming galaxies by foreground galaxies can be used as a probe of dark matter halo substructure. We find that spatially resolved spectroscopy of lensed sources allows dramatic improvements to measurements of lens parameters. In particular we find that modeling of the full, three-dimensional (angular position and radial velocity) data can significantly facilitate substructure detection, increasing the sensitivity of observables to lower mass subhalos. We carry out simulations of lensed dusty sources observed by early ALMA (Cycle 1) and use a Fisher matrix analysis to study the parameter degeneracies and mass detection limits of this method. We find that, even with conservative assumptions, it is possible to detect galactic dark matter subhalos of ∼ 10 8 M with high significance in most lensed DSFGs. Specifically, we find that in typical DSFG lenses, there is a ∼ 55% probability of detecting a substructure with M > 10 8 M with more than 5σ detection significance in each lens, if the abundance of substructure is consistent with previous lensing results. The full ALMA array, with its significantly enhanced sensitivity and resolution, should improve these estimates considerably. Given the sample of ∼ 100 lenses provided by surveys like the South Pole Telescope, our understanding of dark matter substructure in typical galaxy halos is poised to improve dramatically over the next few years.