What to do in the Golden Week holiday?

We will move to Tokyo in March and would be staying there for about 2 years. The Golden Week holiday would be coming soon after we arrive and I was wondering what options do we have during that time. Since it would be a holiday for both of us and our 8 year old daughter, it would be a shame if we don't use the time to explore the country. But, I also don't want to get stuck in massive crowds (as I have been reading online). And since we have to book in advance, now is the time to plan the holiday. I am looking for suggestions that are not extremely crowded and are easy to do with a kid. During the course of our stay in Japan, we will get more opportunities to travel in future, but how can we make the most of this holiday time and visit one or two destinations. We have not visited any place in Japan and this would be our first visit. Please give some ideas for 3-5 days trip starting from Tokyo.
I am severely confused about what to do!

It's kind of late to be planning for the Golden Week, at least for the popular destinations. You may want to consider touring within Tokyo (there are lots to see and do) or nearby day-trip destinations. What sort of activities does your family enjoy (nature, museums, amusement park, onsen, etc.)?

Thanks for your answer. Yes, visiting places within Tokyo is an option. We enjoy nature the most. Any place that has beautiful landscapes and natural beauty. We are not much into museums, architecture or temples. What are the day trip options from Tokyo for nature lovers?

Zoo(動物園/doubutuen) and Aquarium(水族館/suizokukan) are good for family with child.
http://www.jaza.jp/z_map/z_seek03z.html
http://www.jaza.jp/z_map/z_seek03a.html
Especially in Children's day (5 May) some spots enter fee is free for only child.
https://en.wikipedia.org/wiki/Public_holidays_in_Japan
This list is last year 2016 GW's. (not all just major spots listed)
http://cheersmama.jp/?p=10754
Tokyo : 東京 (関東地方 : Kanto region)
http://www2m.biglobe.ne.jp/ZenTech/japan/image/Map_of_Kanto_region.png
https://en.wikipedia.org/wiki/Prefectures_of_Japan
https://en.wikipedia.org/w/index.php?title=Kant%C5%8D_region&oldid=764...

"キッザニア/kidzania" also good and very famous but booking hard usual.(as in long holidays)
http://www.kidzania.jp/tokyo/en/

Tokyo walker (famous local info magazine) web provide a lot of worthful spots.
http://www.walkerplus.com/spot_list/ar0313/
In GW a lot of big special events scheduled no worry.
Search at Google "2017 GW 関東(or other near redion, prefcture) イベント" in mid APR.

BTW, no IDP(Car rent self drive)?

Thanks for all the information and insights. Yes, we can consider driving/renting a car as we have international driving permit which would be valid during that time.