Overall crime rates in San Diego have been in a steady decline for a number of years (for both violent and non-violent crimes). As is typical with any major city, the more densely populated, urban areas tend to maintain the highest crime rates, while the more suburban areas remain the safest. Here is a link that breaks down the crime rates by neighborhood: http://www.neighborhoodscout.com/ca/san-diego/crime/.
For further reading (it's a bit outdated now, but still...): http://www.kpbs.org/news/2011/apr/28/low-crime-rates-reported-san-diego/
Hope this helps!
- Ross Anthony