Install bird netting over your apple trees. This often works for squirrels, as well, although they may still go through the trouble of getting to your apples. Even though this method is expensive and sometimes difficult to install, you can use bird netting for several years if you maintain it and carefully store it during the winter.
Install scare tactics on and around your tree. Shiny things such as strips of Mylar or aluminum blowing freely in the wind scare away both birds and squirrels. You can also try putting windmills, shiny balloons, and pieces of string on your tree. Attach these items to the branches on the inside and outside of the tree's crown.
Apply taste and scent repellents to your trees. Those containing the chemical Thiram are particularly effective for squirrels. There are several commercially available repellents for you to choose from and try.
Install additional bird and squirrel feeders around your property and fill them with hard-to-find goodies for these creatures. Keep them full throughout the year to ensure your squirrels and birds start to rely on them as a constant food source. For birds, identify the species that are eating your apples and research the best foods to put in the feeders.
Apply chemical repellents such as methyl anthranilate to your orchard. Choose a product that is registered for use on fruits.