Amsterdam museums

Nor the Amsterdam City Card (EUR 59 for 24 hrs; EUR 74 for 48) nor the nationwide Museumkaart (EUR 59) seems to be a good deal if these three are the only museums you want to visit.
And I wouldn't buy a public transport card. Not the least attraction of Amsterdam is the city itself. The best way to appreciate it is by walking. The historical part of the city is very compact: from the central station to the Rijksmuseum is a less than 45 min walk.
That's also the thing I'd do upon arriving. Stretch your legs. Orientate yourself somewhat. Get the feeling of the city.

A boat ride on a canal is a good way to see a bit of the city and it is pretty relaxing.

First, WHEN are you going to be in Amsterdam - month and weekdays? And where are you staying?
I ask, because cold temps, wind, and rain might dissuade you from walking long bouts. We just returned in November from our third trip to Amsterdam - 2 fall trips, 1 winter trip. This was the first time we used trams a lot and it was a big time saver and easier on the feet. We still walked around to browse. Multiple day transport passes are available through GBV but you can't use them on the train to/from Schiphol. Unless the weather is horrid when you get there you are probably going to want to spend a good chunk of your time outdoors exploring.
It takes 4-5 museum visits before the museumkaart pays itself off, so you are better off just pre-purchasing tickets if you are only going to three.
You might also want to consider adding in a visit to at least one of the famous canal houses. I highly recommend 1) Museum Van Loon - the most interesting to me as it also has a carriage house beyond the gardens, or 2) Willet-Holthuysen.
If weather allows, nothing beats strolling the canals and streets of Amsterdam. We did that even in winter, ducking into shops when the wind and cold drove us in.
Arrival day is different for us as we rent an apt. This requires a trip to the grocery (which is an interesting outing just to see the differences) but a GREAT treat for you would be a walk along the Prinsengracht to Winkel's 43 by Noorderkerk for some apple pie. I'm tellin' ya, it is the best apple pie you will ever put in your mouth and not to be missed. Then stroll. The lit canals are lovely at dark.
We love open air markets and our favorite is the Noordermarkt (by Winkel's) which occurs on Saturdays. It is open Monday also but didn't seem as well attended by vendors. The Albert Cuyp market is open M-Sa and a fun time as well. If you go there make sure to have a stroopwaffel. These are just possible suggestions as wonderful fillers for your trip.
Three very good restaurants in the city center are Cote Ouest (french bistro style), Cafe Bern (swiss fondue and entrecote), and Haesje Claes (traditional dutch and varied).
Have a marvelous time!

Thank you Nance for great suggestions; I really appreciate recommendations of sights and restaurants. Côte Ouest unfortunately closed... "On January 15 we close the door of our beloved restaurant for good...thank you from our hearts for all visits, big and small..."

Oh, thank you for letting me know that. What a shame. We loved that restaurant.