Entanglement between two qubits (two level atoms) mediated by surface plasmons in three-dimensional plasmonic waveguides is studied using a quantum master equation formalism. Two types of waveguides, a nanowire and a V-shaped channel cut in a flat metal plane, are considered. The Green functions for the waveguides, which rigorously describes the dissipative qubit environment, are calculated numerically using a direct finite-difference time-domain (FDTD) solution of Maxwell's equations. Finite-length effects are shown to play a crucial role in enhancing entanglement, and resonant-length plasmonic waveguides can provide higher entanglement between qubits than infinite-length waveguides. It is also shown that coupling slots can improve entanglement via stronger qubit-waveguide coupling, for both the infinite- and finite-waveguide cases.