I built the same trailer that Nightshade did and used 27" wheels. It did just fine. Smaller wheels will allow you to lower the center of gravity and they will take side loading better. But I always believe in "run what ya brung". Do what you can with what you have and keep on rolling. In my area 20" wheels aren't hard to come by at all. You just pick them out of the trash, along with the rest of the broken BMX bike.
Nightshade's link works fine for me. Run a google search for Mother Earth News Bike Trailer.
Aaron