There is no one best kind of exercise. The key is to find an activity that is comfortable for you and you enjoy doing. Generally, PKD patients can do any activity they want unless they get blood in the urine or it causes back, flank, or abdominal pain. The exercises that are least jarring to the kidneys include walking, swimming, and biking.
Be sure to talk with your doctor before starting an exercise regimen, as they may have guidance about what will be most effective for you or what to avoid. Remember, always stay well hydrated when exercising, and do your best to be active on a regular basis.