You have to understand the differences between a city like Tokyo (large amount of organized crime) and a city like Portland. There is *bound* to be violence when you put a lot of powerful criminals in a small area.
The thing is most of this crime is between criminals. Yes, occasionally someone else ends up shot too but this is a very uncommon event, especially when you consider the population of Tokyo. The chances of being "caught in the crossfire" in Tokyo are much smaller than Portland. Run the numbers -- on a per capita basis of course.
I don't like Tokyo myself and have no desire to live there. However if given the choice between Tokyo and Portland it would be a no-brainer. Even if the pay/job in Portland was better I would not move my family to the US. I have no desire to live in the current American climate.