Raven Tools has created a great little website that can help you create some code for tracking affiliate links in Google Analytics.
To track affiliate links in Google analytics you need to use the Event Tracking feature inside Analytics. This is slightly more complex than your generic goal tracking. And this is why Raven Tools has created this handy website!
All you need to do is fill in the details on the ‘GA Event Tracking Code for Affiliate Links’ page and it will generate the code for you.
From there all you need to do is add this code inside your affiliate links (examples are shown on the site).
Now see the tracking inside Analytics, just navigate to: Behavior > Events > Overview
It will take at least a day for some stats to show up.