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This paper formulates an optimal control problem for a system of rigid bodies that are neutrally buoyant, connected by ball joints, and immersed in an irrotational and incompressible fluid. The rigid bodies can translate and rotate in three-dimensional space, and each joint has three rotational degrees of freedom. We assume that internal control moments are applied at each joint. We present a computational procedure for numerically solving this optimal control problem, based on a geometric numerical integrator referred to as a Lie group variational integrator. This computational approach preserves the Hamiltonian structure of the controlled system and the Lie group configuration manifold of the connected rigid bodies, thereby finding complex optimal maneuvers of connected rigid bodies accurately and efficiently. This is illustrated by numerical computations.