A service charge is included in the basic room rate at most ryokan. Because tips are not expected, you need not worry about tipping for services rendered.
Nevertheless, while tipping is not customary in Japan, the ryokan is sometimes an exception. When the nakai or okami brings a snack or tea on the first evening, you may tip them anywhere from 1,000 to 3,000 yen. You may also tip as gratitude for exceptional service. Tips should be given in an envelope or wrapped in paper (even a tissue) and presented with both hands.