Berliners usually chose a kindergarden that is in their "kiez" (neighborhood) and only travel further afield if they are looking for something special i.e. Waldorf or a bilingual kindergarden. This is because the local kita's seem to do just fine. My advice is to first find a neighborhood and apartment that suits you and then walk around the area to see what is available.
Or, you could take a look at this list of kita's, broken down by neighborhood:
www.kitanetz.de/bezirke.html
I would say there are many child friendly neighborhoods in Berlin. Urban areas like Prenzlauerberg & Charlottenburg are nice but if you prefer more residential neighborhoods then
Zehlendorf or Kladow just to name a few.
Wikipedia has decent write ups and descriptions of the various Berlin boroughs, fyi.