None of those places are what most people would consider "affordable". Ballard and north Queen Anne are both very popular neighborhoods, and housing costs reflect this, however I would imagine Ballard being slightly less expensive. I would very strongly advise you against living in downtown Seattle, especially with children, because it is the most dangerous area in the city - and also ridiculously expensive. Most people work in downtown but don't live there.
You can use this site to view housing values:
http://www.neighborhoodscout.com/wa/seattle/ and there are also options for schools and safety. Generally, north Seattle neighborhoods are safer but more expensive than south Seattle neighborhoods. For an affordable, safe place to live with good schools, I would actually recommend Shoreline which is just north of Seattle proper but still a very short commute to most of the city.
