An unsupervised machine learning strategy is developed to automatically cluster the vortex wakes of bio-inspired propulsors into groups of similar propulsive thrust and efficiency metrics. A pitching and heaving foil is simulated via computational fluid dynamics with $121$ unique kinematics by varying the frequency, heaving amplitude, and pitching amplitude. A Reynolds averaged Navier-Stokes (RANS) model is employed to simulate the flow over the oscillating foils at $Re=10^6$, computing the propulsive efficiency, thrust coefficient and the unsteady vorticity wake signature. Using a pairwise Pearson correlation it is found that the Strouhal number most strongly influences the thrust coefficient, whereas the relative angle of attack, defined by both the mid-stroke and maximum have the most significant impact on propulsive efficiency. Next, the various kinematics are automatically clustered into distinct groups exclusively using the vorticity footprint in the wake. A convolutional autoencoder is developed to reduce vortex wake images to their most significant features, and a k-means++ algorithm performs the clustering. The results are assessed by comparing clusters to a thrust versus propulsive efficiency map, which confirms that wakes of similar performance metrics are successfully clustered together. This automated clustering has the potential to identify complex vorticity patterns in the wake and modes of propulsion not easily discerned from traditional classification methods.