You can try cleaning his ears with a Q-tip and some ear cleaning solution. Our Yorkie guidebook says you can use ear-cleaning solution available from the vet or a pet store (we bought some from Drs. Foster and Smith, and we've seen it at pet stores), or maybe even just a little water. Here's what the book says about ear care:
"Using a Q-tip is the easiest way to keep ears clean. Be sure you use a separate Q-tip for each ear. Dip the Q-tip in an ear cleaning solution available from your veterinarian. This ear rinse will break up any wax that may have accumulated inside the ear. Or you can dribble a few drops of the solution directly into the ear. Cover the ear with a cotton ball or two, as your Yorkie will probably shake her head. Grasping the sides of the ear gently, squeeze the folds together up and down. You will hear the liquid make a squishing sound. This loosens the debris. Use a Q-tip or a small piece of cotton to clean the area. If you notice dark brown or black debris on the cotton, a bacterial or yeast infection or ear mites is a possibility. Repeat this procedure the next day and continue until the cotton comes out clean. Be sure to dry the ear thoroughly each time you use the ear rinse.
If you are afraid you will puncture your dog's eardrum by using a Q-tip, don't worry. While the ear canal is at the base of the actual ear, the eardrum is actually located much farther down and out of reach.
If your Yorkie yelps a bit when you clean her ears, that means the solution feels cold and she isn't accustomed to the sensation. If an infection is present, the area is probably sensitive and the cleaner may sting a bit.
If you see your Yorkie shaking her head or scratching at her ears several times, she may have ear mites..."
Hope that helps. One of our boys is always scratching at his ears, too, but the vet has never seen anything wrong with them. Hopefully that's the case with Jake, too!