Puppies ears should be cleaned regularly to ensure the ears are kept clean and to accustom your puppy to having his/her ears touched and treated. It is especially important to clean ears if they get very dirty. The dirt inside the ears can be due to a normal waxy discharge, or abnormal discharges due to an underlying infection (e.g. earmites, bacteria, yeast). If your puppy is shaking its head very frequently, scratching at its ears and appears distressed when you try to touch its ears - it may have an infection. In this case, your puppy will need to see a veterinarian for the appropriate treatment.
Do not wash the ears with water as this can actually lead to an infection. Be careful when you are bathing your puppy as well, to make sure water doesn't get into the ears. If you wish, there are special ear washes available from your veterinarian to ensure that your puppy's ears stay clean and healthy. These can be used after swimming or bathing.
If your puppy has hairy ears, which is common in some breeds (e.g. poodles), plucking the hairs out of those ears is not recommended at all, unless there is already an infection at the time. In a normal ear, if the hairs are plucked out, this will lead to oozing and bleeding (and is painful for your puppy too!). The oozing and bleeding can actually lead to an infection due to the moisture present in the ears. However, if your puppy's ears are infected, then the hairs may be removed to get all the discharge out of the ears and help get the medications into the ears properly. If in doubt, speak to your local veterinarian for advice.