Go to Hyperdia.com.
Click on ‘More options’.
Note: You need to pay the cost of using Private lines separately.
Since Rinkai Line (based on the example figure above) is a private line, you will need to buy a separate train ticket from Osaki Station going to Tokyo Teleport Station which costs 330jpy. Osakajokitazume to Osaki station is covered by JR Pass.
You may also check this 9D10N detailed budget itinerary for Japan. It covers tourist spots in Nagoya, Osaka, Kyoto, Tokyo, Hiroshima and Fukuoka.