We compute both electron and phonon transmissions in thin disordered silicon nanowires (SiNWs). Our atomistic approach is based on tight-binding and empirical potential descriptions of the electronic and phononic systems, respectively. Surface disorder is modeled by introducing surface silicon vacancies. It is shown that the average phonon and electron transmissions through long SiNWs containing many vacancies can be accurately estimated from the scattering properties of the isolated vacancies using a recently proposed averaging method [Markussen et al., Phys. Rev. Lett. 99, 076803 (2007)]. We apply this averaging method to surface disordered SiNWs in the diameter range of 1–3 nm to compute the thermoelectric figure of merit ZT. It is found that the phonon transmission is affected more by the vacancies than the electronic transmission leading to an increased thermoelectric performance of disordered wires, in qualitative agreement with recent experiments. The largest ZT>3 is found in strongly disordered 111-oriented wires with a diameter of 2 nm.