Electrical impedance tomography (EIT) is a badly posed inverse problem, but can be stabilized if one assumes that the conductivity is piecewise constant, with a relatively small number of distinct regions, and that the region boundaries are known, for example from prior anatomical imaging. With this assumption, we introduce a three-dimensional (3-D) boundary element method (BEM) model for the forward EIT map from injected currents to measured voltages, and 3-D inverse solutions for both BEM and the finite element method (FEM) which explicitly take into account the parameterization implied by the known boundary locations. We develop expressions for the Jacobians for both methods, since they are nonlinear, to more rapidly solve the inverse problem. We show simulation results in a torso geometry with the heart and lungs as inhomogeneities. In a simulation study, we could reconstruct the conductive values of some internal organs of a human torso with more than 92% accuracy even with inaccurate internal boundary locations, a randomized rather than constant conductivity profile (with the standard deviation of the Gaussian-distributed conductivities set to 20% of their mean values), signal to measurement noise of 50 dB, and with different meshes used for the forward and inverse problems. BEM and FEM perform similarly, leading to the conclusion that the choice between them should be based on secondary considerations such as computational efficiency or the need to model conductivity anisotropies.