We just got back from 10 days in and around Krakow, Poland with our toddler DD. It was awesome. Krakow might be a bit of a trip from Berlin, so I would suggest the Bavaria region of Germany. The kids would love the castles, especially your 6 yo. Most places aren't easy to get to without a car though, but it's definitely worth the trip.
I would also suggest Vienna, Austria if you are looking for a trip that would end at a good location with an international airport. The city is beautiful and the airport is one of the easiest I've dealt with. If you decide to do that, then Prague is right on the way by train. I think your challenge will be to narrow down your choices

have fun OP!