Not sure if this will help but we've been to several Christmas markets in the past in Germany and other countries.
I'd advise that you go mid-week as at weekends they are very, very busy. We went to the one at Lille (northern France)on a Saturday a couple of years ago and couldn't even walk around it let alone stop at the stalls. We had a pushchair with us which was a huge mistake. The children hated it as they couldn't see anything and were being pushed and jostled the whole time.
In Germany, Munich is a good place for Christmas markets and there are several around the city. However, the big one in the Marienplatz gets extremely crowded.
The one at Lübeck (near Hamburg) was good as was the one at Karlsrühe (which is closer). Nürnberg is meant to be one of the best but I haven't been there.
A big problem we find with Christmas markets is that they are so expensive (and a lot of the things being sold are tat). Yes, there are lovely candles and nativity scenes and biscuits and decorations but you pay a fortune for them. The best bit is the glühwein but it's strong stuff!
I personally wouldn't take my almost 3 year old specially to a Christmas market although my 5 year old twins probably would be old enough to handle the crowds now. I definitely wouldn't go at a weekend.
Sorry if this sounds negative - it's not meant to be and we had some lovely weekends away in Germany visiting Christmas markets before we had children.
Maybe other mumsnetters have had better experiences than me with children?