The eBay affiliate program currently works on a PPC (pay per click) basis, so you get paid every time a reader clicks on the link -- just like AdSense. The Amazon affiliate program works on commission, so you only get paid if someone actually orders an item.
So if you have a lot of readers but the content of your article doesn't match up with high value items, eBay will probably make you more money. However, if you have readers willing to purchase expensive things, you may get more commission from Amazon.
The general consensus is that people having been earning more from eBay than Amazon. However, you can stack both, so the MOST profitable thing is to do both!