The design of thermoelectric materials for the efficient conversion of waste heat into electricity requires simultaneous tuning of their electrical and thermal conductance. A comparative theoretical study of electron and phonon transport in thiophene and ethylenedioxythiophene (EDOT) based molecular wires is performed. It is shown that modifying thiophene by substituting ethylenedioxy enhances the thermoelectric figure of merit ZT for molecules of the same length. Furthermore, it is demonstrated that the electrical conductance of EDOT-based wires decays more slowly with length than that of thiophene-based wires and that their thermal conductance is lower. The room-temperature ZT of undoped EDOT is found to be rather low. However, doping of EDOT by the electron acceptor tolunenesulfunate increases the Seebeck coefficient and electrical conductance, while decreasing the thermal conductance, leading to a thermoelectric figure of merit as high as ZT = 2.4.