Hard to know where to start....... It's a great place.
Tokyo is almost a given, but not compulsory. One word of caution however: you WILL feel like an itsy-bitsy ant in an enormous anthill. It is mind-bogglingly crowded, though Japanese courtesy and their highly-developed etiquette makes life bearable. If you include Tokyo, the only recommendation I will make - and one that your kids will love - is a visit to the 'Robot Restaurant' in Shinjuku. Completely, utterly bonkers. There simply isn't a more fun way to go deaf.
Beyond Tokyo, consider Kyoto for its culture and history and Miyajima Island for sheer beauty, albeit in a touristy fashion. If you do visit Miyajima, I recommend staying on the island itself for a couple of nights. It is transformed each evening when the visiting tourists all head back to their mainland hotels. Watching the sun go down behind the Torii gate is very special, as is a cable car ride/walk up to the numerous lookouts. Most people combine a visit to the island with a day in Hiroshima, because they are nearby. I found a visit to the Peace Park very, very moving, so it won't be everybody's cup of tea.
Finally, do try to include a trip on the bullet train (Shinkansen). We used it to transfer between Tokyo, Hiroshima and Kyoto. It's another experience the kids might enjoy. No trip on the Shinkansen is complete however, without a bento box lunch on board (best purchased in the station before boarding).