Amsterdam for 5 nights

Last year we used VRBO and rented a house in Zandaam.
Zandaam is about 15 minutes from the Centraal Station. The area was very typically Dutch and our house was a five minute walk from the station. Would stay there again.
The children will enjoy Zaans Shans.
It is an excellent outing complete with working windmills, farm animals, wooden shoe making and cheese sampling.

Lots of attractions for kids:
Nemo Science Museum, the Maritime Museum, Zoo, Micropia, This is Holland attraction.

Zaanse Schans has windmills, a blacksmith, etc. and is a recreated historic village not far from the city.
For a more authentic experience, ( the famous ones which you alluded to) take a train to Rotterdam and a water bus to Kinderdijk, 19 windmills in their original locations. You can rent bikes there to ride past them or walk. Beautiful spot. .
Amsterdam is not large and trams take you all over the city. We like the Central Canal Ring area or Jordaan.

I like Hotel Brouwer on the Singel canal - a five minute walk from Central Station. Their website states they are under reconstruction with a reopening in June of 2019.....my calendar says this is July, so you if you are interested, you can contact the proprietor, Michelle, at her email for an update. michelle@hotelbrouwer.nl
This is a small boutique hotel - they are not listed in the big travel search sites, although RS recommends them. Our room was around $150/night last April during "tulip time".

If your children can share a double bed, Studio Inn (a B&B) in Westerdok area might work for you. My wife & I stayed there with our adult child for six nights recently. You have your own upstairs area with two bedrooms and a bath with shower. The larger bedroom has a double bed, breakfast table (4 chairs), and reading chair (no TV or A/C). Every morning your host Guido brings you a nice continental breakfast, and probably will take requests if your children prefer certain foods. There is a nice children's playground across the street. We enjoyed returning each evening to a quiet residential area with many nearby restaurants. Your children might enjoy watching the river traffic if you can get a picnic table by the water at nearby Meneer Nieges restaurant (not sure if they have a kids menu). Transportation is good as around the corner from Studio Inn is the stop for bus 48 to nearby Central Station (stay on the bus for Nemo Science Museum and Maritime Museum), and you have a short walk to Tram 3 turnaround which takes you to Museumplein. We got IAmsterdam cards (offices at airport or Central Station) which provided museum admissions and transportation use. Once you have the cards, you can make online timed reservations for Van Gogh Museum. Also the card works for multiples of 24 hour periods, so we could start using the five-day card Thursday @ 11 AM and still use it on the bus to Central Station with our luggage on Tuesday morning (the day passes end at midnight). Take your children by the hand and look both ways before crossing, as those bicycles don't stop!