Very difficult question to answer when I don´t know your family´s likes, dislikes, hobbies, touring style, etc. Do you vacation often? Have you visited many other countries? Do you live in the USA? Would this be a "once in a lifetime" trip abroad for you?
I love Disney, but I also really liked Prague and will most definately visit the city again some day. We went with 3 kids who were 2,8 and 10 at the time and we all had a great time. Prague is a beautiful city with lots of history and architecture. It is very different from any city in the US I´ve ever visited. We rented an apartment for our stay there, very central and very convenient. We had a car but hardly used it at all while in the city. We came driving from Denmark and then went on to Croatia, Bosnia and Hungary. It was an awesome trip and we still talk about it a lot.
That being said, Disney is very special as well and definately not "just another themepark" (I address this in my blog, see siggy below). It is a happy place with a great atmosphere, but you have to "let" yourself experience the magic and somewhat become a child again. If either you or your husband go thinking that this is just fun for your child and that this trip is for her, you definately won´t enjoy it as much as Prague.
Do some research on both places. Try to make a rough itinerary of what you would do in Prague and what you would do at Disney and then make your decision based on that.
Happy planning, whatever you decide
