In this work, we propose a novel computational BEM-FEM model for treating the 3D, unsteady, fluid-structure interaction (FSI) problem related to the hydroelastic performance evaluation of passively deforming wings operating as marine thrusters that undergo prescribed flapping motion. The elastic response of a wing, fully submerged within the fluid medium, is implicitly dependent on the hydrodynamic pressure and vice-versa. We implement a strongly coupled, partitioned scheme to tackle this implicit non-linearity. The model couples an unsteady boundary element method with finite elements based on Discrete Kirchhoff Triangles for thin plates with stiffness variation. The cost-effective nature of this methodology enables fast analysis of morphing bio-mimetic thrusters. The solver is compared against other models and available experimental data for verification. Finally, the FSI solver is used to investigate enhancing the efficiency of an autonomous underwater vehicle thruster via tuning the elastic parameter..