An error minimization method is presented for Stokes polarimeters applicable when the detected signals are affected by a combination of shot and Gaussian noise. The expectation of the Stokes vector variance is used as a performance measure. This measure is compared with the condition number of a polarization state analyzer matrix that is commonly used as a figure of merit. We show that a polarimeter with the minimum condition number is not necessarily optimal. The approach is used to optimize existing prism based polarimeters giving improvements in the performance when shot-noise cannot be neglected.