The kinetic boundary condition for the Boltzmann equation at an interface between a polyatomic vapor and its liquid phase is investigated by the numerical method of molecular dynamics, with particular emphasis on the functional form of the evaporation part of the boundary condition, including the evaporation coefficient. The present study is an extension of a previous one for argon [Ishiyama, Yano, and Fujikawa, Phys. Fluids 16, 2899 (2004)] to water and methanol, typical examples of polyatomic molecules. As in the previous study, molecular dynamics simulations of vapor-liquid equilibrium states and those of evaporation from liquid into a virtual vacuum are carried out for water and methanol. In spite of the formation of molecular clusters in the vapor phase and the presence of the preferential orientation of molecules at the interface, essentially the same results as in the previous study are obtained. When the bulk liquid temperature is relatively low, the evaporation part is the product of the half range Maxwellian for the translational velocity of molecules of saturated vapor at the temperature of the bulk liquid phase, the equilibrium distribution of rotational energy of molecules at the temperature, and the evaporation coefficient (or the condensation coefficient in the equilibrium state). The evaporation coefficients of water and methanol are determined without any ambiguity as decreasing functions of the temperature, and are found to approach unity with the decrease of the temperature.