So happy for you to visit one of my favorite cities on the planet. We were there again back in December and had a marvelous time. I visited with my godson when he turned 16 a few years ago and he loved it. I'm cutting and pasting from an email to my sister-in-law who asked me for info as she is going soon, too. Here are a couple ideas:
This is a pretty great website for general info: https://www.holland.com/global/tourism.htm For specific Amsterdam info, this is a good site: https://www.iamsterdam.com/en Look for info on the trams - they are super easy and convenient way to get around town. The subway just opened but we've never used it - yet. As many times as I've been to Holland, I've never had to rent a car.
Anne Frank House is a must. The museums you've listed are very good but not too sure how much your teenager will enjoy them unless she is into art. On the flipside, my godson happens to like Von Gogh and thoroughly enjoyed the museum. I highly recommend the Verzetsmuseum (www.verzetsmuseum.org) or Dutch Resistance Museum. It is small but fascinating.
Have you been to Colonial Williamsburg in Virginia? The equivalent in Holland is Zaans Schans (https://www.dezaanseschans.nl/en/). It is an interesting day outside the city. My godson still talks about it. You can easily reach it via train/tram from the city.
One of my favorite spots in the city is Vondel Park. Not sure about the weather when you'll be there, but during the summer it is full of people. Outside the park and 3-4 long blocks from the Museumplein is my favorite little local non-tourist cafe: Cafe Gruter (http://cafegruter.com/en/). I literally can't count the amount of time I've spent here. In the last 2 years, three other friends have also visited and loved it. There are two Dutch snacks that are to absolutely die for that are very good at Cafe Gruter: Bitterballen and Kaastangels. Trust me, your daughter will especially love the Kaastangels. One of my friends was there this past summer and his 15 year old son raved about the burger.
One of the awesome foods that you can get in Holland is Dover Sole and seems to be served in many places. It is much less expensive than in the US. It is one of our favorites. The most exclusive (and phenomenal) seafood restaurant is called Lucius Visrestaurant (https://lucius.nl/en/reservation/). If you decide to go, make sure you get a reservation. They have the most unique broth based lobster bisque that we've ever had. Amazing.
Literally down the street from Lucius, is a narrow bar that is owned by the next door restaurant. We found it by accident on our last trip. The name of the bar is Café De Koningshut (https://www.haesjeclaes.nl/koningshut/). They will bring the food from the restaurant to the bar. The Dover Sole there was incredible!
If you guys want a day "at the Shore", consider taking a day trip to The Hague (Den Haag) and go to Scheveningen Beach. We visited once in spring and always said we would go back if we were there in the summer. It is about a 50 minute train ride from Amsterdam and around 25 Euro for a round trip. If you want a "down" day on your trip, I'd totally spend a day here depending in the weather.
WATCH OUT FOR BIKES! They have the right of way!