The thermal conductivity of vitreous silica is computed using the direct method in molecular dynamics simulations with three sets of empirical force fields, including the BKS, Teter, and ReaxFF, to investigate their performance in thermal characterization. Various heat flux and system sizes are used in the simulations to evaluate the statistical uncertainty and the finite-size effect. While all these potentials can reproduce realistic silica structures, the ReaxFF provides better agreement with experiments at 300 K than the BKS and Teter, which is due to its improved description of low-frequency vibrations. Increasing the heat flux and cross-sectional area tends to reduce the calculated standard deviation induced by thermal fluctuations, thus contributing to more accurate thermal conductivity predictions.