Skip the red light district, the atmosphere of creepy guys who are window shopping is very unpleasant to submerse yourself in. That said, this will probably be your only time to see the district since there are advanced plans to relocated it to a different part of Amsterdam (out of the city center).
Enjoy Anne Frank's house. Make sure you arrive early, even if you have purchased the tickets in advance. The canal tour on a boat is a great way of viewing the houses along the canal cause the perspective you'll have can only be seen from the water. On the street level you are too close to the buildings, messing up the perspective. Try to go on a non-rainy day. The boats are covered / have a transparent roof, so rain will prevent you from seeing what you came for.
If you like chocolate, visit Puccini. A bit expensive, but really nice bonbons (friends, help me out here, how the hell do you translate bonbons to English?!). Don't fall for the tourist traps that try to sell you cheese. Of you want cheese (probably not since you're going on a cruise afterwards) visit the areas outside of the city center to find cheaper - and much better quality - cheeses.
Since you only have two days, I'm going to leave out the other museums. Just walk around, be mindful of the red biking lanes and enjoy. If you're an adult, try smoking one of them special rolled cigarettes or, alternatively, eat some of the special brownies. Cause hey, when in Amsterdam right?
I hope you will have a great time!
(I kid I kid). Locally they have good Jenever (Genever), which is kinda between Gin & Whisky. There are many different distilleries in the Netherlands & Belgium (+ France & Germany). I unfortunately don't know much more about dutch booze, because I rarely buy alcohol in the Netherlands (and actually do buy my beers from here in Belgium, or my wine from France 