Blood flow computations in complex geometries are of major interest in various cardio-vascular applications. However, deriving an appropriate computational model is still an open issue and a central question is how to incorporate and quantify uncertainties due to different modeling assumptions. The present work is intended as a first step in this direction, in the particular case of blood flow in the cerebral venous system. After a careful evaluation of the influence of the computational methodology, the study investigates the impact on the velocity field and the wall shear stress of three inflow boundary conditions, two strategies for treating the outflow boundary condition and two different viscosity models. The results demonstrate that the effect of setting the inflow boundary condition on the forces created by blood flow, is likely greater than for other modeling assumptions, the other important factor being the blood viscosity model, especially in wall shear stress computations. They suggest that improvements on the one hand on the mathematical and computational approach, and on the other hand on available data for their treatment are needed.