You might want to post this question in the Netherlands section of "Destination Q&A" to get more responses.
We had a good canal cruise with the Blue Boats starting near the Rijksmuseum, but there are alternatives with different starting points. It's certainly a good use of time but I don't think it matters much which company you use.
Besides the museums you mentioned, we were impressed by the Dutch Resistance Museum, which treats the WWII experience in a relatively sophisticated way, making clear that most Dutch people didn't "resist" but just kept their heads down, while others collaborated and others actively resisted. We also enjoyed visiting the Hermitage Amsterdam, with a special exhibit of impressionists (on loan from the St. Petersburg Hermitage) and a better exhibit focused on the civic militias of the Dutch Golden Age. You might want to see what will be there during your visit.
If you like cats, you might try the Kattenkabinet, a museum all about cats, with its own feline resident population. Allergy sufferers like my cat-loving wife need to medicate well in advance. ;-)