Apple cider vinegar (unfiltered variety) works wonders. You can use it in the ears, as a body rinse, and you can add it to their food and water. Sometimes though, if the yeast has gotten really bad, you may need a non home remedy approach to get things under control.
For a shampoo, I highly recommend Eqyss Micro-tek ... It is a horse shampoo, but the company does have a dog variety as well...same formulation for both though. It works wonders on skin conditions and is gentle enough to use regularly without drying the skin.
For ears, my favorite yeast buster is Zymox Otic HC 1% solution. It has worked better than prescription products and is truly amazing stuff!