Is there a good sourcebook that describes typical city organization from the government to the local police and the militia/military as well as its ties to the state governments?
It depends on how involved you want to get or the exact info you need. GameMastery Guide has some nice base info but to get into really in depth stuff you could check out A Magical Medieval Society - Western Europe (2nd edition).
http://www.rpglibrary.org/utils/meddemog/ is a nice site to get some rough numbers for various kinds of things within a settlement. It is based on Medieval Demographics Made Easy by S. John Ross.
These are just some of the resources out there. If you have more specific questions on the topic please feel free to ask away.
For medieval fantasy, you might want to check out "A Magical Medieval Society: Western Europe" from Expeditious Retreat Press. That's a pretty thorough treatment of the Manor system, cities, and country life for a fantasy region in D&D 3.x based on Germany in the middle ages.
That being said, there's a lot of variation from culture to culture, so you could probably find dozens of history books providing a view like that about one region at a time.
This is a free sample chapter of the Magical Medieval Society on cities
The full book is here
and the rest of their sourcebooks from the same set are here
The Pathfinder GameMastery Guide also goes over all the subjects you're inquiring about as well. It is a really good source book to start with since it is already geared towards Pathfinder. They use real world history and examples to help guide you along the way - a very good product.