Hi Samuel,
in short, Google Analytics is accurate enough, and here are a few suggestions to address your discrepancy concerns:
1. The number of visitors you mention is not large enough to make conclusions about the accuracy of this or that tracking system.
2. Google Analytics might not track visitors if they don't have java script set or if they block Google Analytics. As a result, Google Analytics reports on a fewer number of visitors.
3. Your affiliate stats, on the contrary, might track not only java script but also robots that index your website. As a result, your affiliate stats reports on a larger number of visitors.
Happy ranking!
