My advice is to do it in-house. Most of my past startups have been very affiliate driven and I have had some bad experiences outsourcing (most commonly that the checks get sent late). The most important thing to an affiliate is that they are paid on time every time.

If you think it will be too much of a hassle, there are several companies that provide this service. Here is one: http://www.webmasterchecks.com/index.html