How about visiting Tokyo Sky Tree? The observatory would be enjoyable, and there are also some attractive institutions for kids such as aquarium and planetarium. It's also a great shopping place, too so I recommend it for family with kids.
There are great aquariums and amusement parks in Tokyo. For example, Sunshine Aquarium in Ikebukuro, Shinagawa Aquarium in Shinagawa, Hanayashiki amusement park in Asakusa, or Tokyo Disneyland.
Tokyo Edo Museum in Ryogoku might be another fun place. At the museum, you can learn the history of Tokyo and there are lots of exhibitions where people can touch and feel. National Museum of Nature and Science in Ueno is another great place.
Ueno has the first zoo in Japan where Giant Panda is the most iconic animal. The zoo is very big so you can spend a day there, too.
How about experiencing cooking udon noodles and origami? Hub Japan offers the plan to experience both of them and that is available also for kids over 3 years old.