Bio-inspired thruster designs based on flapping-foils have the potential to achieve high efficiency and stealth, thus allowing for an extension of the overall operational capabilities of autonomous underwater vehicles (AUVs) propelled solely using foils. In this work, we produce thruster designs with enhanced propulsive performance by introducing prescribed chordwise and spanwise changes in the geometry during each flapping-cycle, i.e. active morphing, with optimally tuned parameters to further mimic aquatic locomotion. The reference design performs a thrust-producing combination of out-of-phase heaving and pitching motions, whereas for the evaluation of each candidate design, a cost-effective GPU-accelerated boundary element solver (BEM) is proposed.