The geodesy of irregularly shaped small bodies presents fundamental challenges for gravitational field modeling, particularly as deep space exploration missions increasingly target asteroids and comets. Traditional approaches suffer from critical limitations: spherical harmonics diverge within the Brillouin sphere where spacecraft typically operate, polyhedral models assume unrealistic homogeneous density distributions, and existing machine learning methods like GeodesyNets and Physics-Informed Neural Networks (PINN-GM) require extensive computational resources and training time. This work introduces MasconCubes, a novel self-supervised learning approach that formulates gravity inversion as a direct optimization problem over a regular 3D grid of point masses (mascons). Unlike implicit neural representations, MasconCubes explicitly model mass distributions while leveraging known asteroid shape information to constrain the solution space. Comprehensive evaluation on diverse asteroid models including Bennu, Eros, Itokawa, and synthetic planetesimals demonstrates that MasconCubes achieve superior performance across multiple metrics. Most notably, MasconCubes demonstrate computational efficiency advantages with training times approximately 40 times faster than GeodesyNets while maintaining physical interpretability through explicit mass distributions. These results establish MasconCubes as a promising approach for mission-critical gravitational modeling applications requiring high accuracy, computational efficiency, and physical insight into internal mass distributions of irregular celestial bodies.