The FBI collects common Uniform Crime Reporting (UCR) data from all municipalities. These include things like murder, rape, assaults, property crimes, vehicle theft etc. Their primary site is here: http://www.fbi.gov/about-us/cjis/ucr/ucr and they have common stats going back decades.
Typically, municipalities use a /1000 population rate which can also be broken down by city, zip, census tract, police beat or similar geographic boundaries. These numbers can be skewed as discussed by a variety of demographic and environmental factors.
When looking at the municipal level there are many other issues such as the codes law enforcement cite the offender with. In California for instance one might be cited under the state Business & Professions Code, Penal Code, Vehicle Code and others are cited under local ordinance (i.e. minor in possession of alcohol). This example also illustrates that the offender might be cited under local or state laws at the discretion of the officer.
Another major factor is the police staffing and service levels. This can vary widely but, is identifiable. The police aren't too keen on revealing these numbers largely I believe out of institutional pride. However, if an area has a higher level of crime it might be partly attributable to low staffing levels. Or, they may have high staffing but, low in-service (available for dispatch to crime) times.
Finally, there has to be a way to somehow regionalize this analysis because in my city (San Diego) for instance, although we have a large population we have abnormally low crime. We also have critically understaffed police because of chronic budget cuts (about 12% understaffed or over 250 officers). One might suggest if we have such low crime why would we need more officers. Another might suggest that fewer crimes are reported because people's tolerance is up (understanding that if they call a cop they'll likely not show up). Other factors include the departmental resources i.e. a low level of Vice officers when compared to staffing standards.
What would be ideal is for municipalities to have a tool to look at similar citizen demographic and police-resourced municipalities that have lower crime rates for certain offenses (i.e. the minor in possession example) and compare their municipal codes. Community leaders might find alternative ordinances that help them reduce those crimes in their areas.
There are other factors relating to business types and densities. Areas with high levels of shopping malls or tourist zones will have higher auto prowls (break-ins) and auto theft. Areas highly concentrated with bars likely have higher levels of DUI incidences but, not high DUI-offense rates because of low DUI patrols etc.
This is definitely complicated and challenging topic but, one that we must work to improve because not only does this improve our ability to pursue happiness in safe communities, people's well-being and lives are on the line.