I agree. Depends on age of kids and both cities are lovely, but Amsterdam is flat, has canals for something a bit different, lots of parks and is quite compact. Prague's a bit more spread out and is cobbley and hilly! Watch out for the cyclists in Amsterdam, though, they give short shrift to pedestrians!!
If so Szecsenyi baths is worth a visit if the kids are old enough. It's got a whirlypool bit that is great fun and the warm spring water is wonderful. We did it in November when it was freezing cold wonderful. It's an experience. Have a look here
DS (20) came back yesterday from a tour of Europe (Paris, Lyon, Florence,Rome, Venice,Vienna, Bratislava, Budapest,Krakow,Prague,Berlin & Amsterdam) - he said Budapest was the best & Bratislava the worst Between Prague & Amsterdam, he preferred Prague - Prague is cheaper, good walks, interesting buildings, better atmosphere but says there's probably more to do with kids in Amsterdam.
Budapest is brilliant for kids, particularly Margaret Island but Amsterdam is fab too - depends on your travel schedule and how you're travelling around. We went to Amsterdam last year and it fitted in well with driving between Antwerp and Hamburg whereas Budapest or Prague obviously further over.
So far we have decided on Tromso, Oslo, Stockholm, Copenhagen, Berlin and finally Paris (inc a night or two in Disneyland). We are only going to have two weeks to fit everything in so are only going to be spending a couple of nights in each place and travelling by train or plane between destinations. We are thinking of adding one more place probably between Berlin and Paris.
Kids will be 9 and 7 and have enjoyed sight-seeing in the past.
Budapest does look great, I think I may try and fit it in even though it is further away than Amsterdam.