Thanks for the data link. I'd consider the difference of 6.1 vs. 4.1 per 100k comparable. I was right about Oakland, though, at 26.3. Even Stockton is higher than SF at 19.7. I'll use that one to back up my fear of bored kids in isolated towns.
The problem in Oakland is gang activity. So your chances of getting randomly killed there are a lot less than the numbers might suggest. However, it does happen that people get caught in the crossfire. Oakland also covers a pretty wide area and there are some better and worse parts.
I have never been to Stockton, but you are right that the crime rate there seems surprisingly high. The cops blame it on the drug cartels. The city is fairly poor (median income 35k) and filed for bankruptcy last year. I'm not sure what the problems are there, but I'm fairly sure bored kids are not near the top of the list.
Incidentally, there is something distasteful about criticizing a city you've never even visited. Especially when you live in a much whiter and richer area. I grew up in a poor area that I'm sure many here would have looked down on. You can have pride in where you live without tearing other people down.