Which cities nearer to shiragawa go

Out of the 3 cities you mentioned, Tokyo is the nearest city to Shirakawa, taking only around 2 hours. You can use the JR rail pass.

For timetables and other ticket prices from Tokyo to Shirakawa, you can click here: http://www.hyperdia.com/en/cgi/en/search.html?dep_node=TOKYO&arv_node=SHIRAKAWA&via_node01=&via_node02=&via_node03=&year=2018&month=02&day=08&hour=09&minute=21&search_type=0&search_way=&transtime=undefined&sort=0&max_route=5&faretype=0&airplane=off&ship=off&sprnozomi=off&lmlimit=null&search_target=route&facility=reserved&sum_target=7

If you are planning to go to Tokyo from Osaka, you can also use the JR pass, but you can’t take the Nozomi trains.

The JR rail pass can’t be used for Mizuho and Nozomi Shinkansen trains, but you can use other Shinkansen trains.

For timetables and other ticket prices for your trip from Osaka to Kyoto, you can click here: http://www.hyperdia.com/en/cgi/en/search.html?dep_node=OSAKA&arv_node=TOKYO&via_node01=&via_node02=&via_node03=&year=2018&month=02&day=08&hour=09&minute=33&search_type=0&search_way=&transtime=undefined&sort=0&max_route=5&faretype=0&airplane=off&ship=off&sprnozomi=off&lmlimit=null&search_target=route&facility=reserved&sum_target=7