There aren’t really any crime ridden ghetto areas in Tokyo as there is in other major cities. Violent crime rate is extremely low in Japan no matter where you’re, in fact you should be more worried about the non-violent crimes(like getting scammed by shady bars in roppongi) rather then being mugged on the street.
However, there are certainly areas where unemployment rate is relatively high and the not so fortunate members of the society congregate. Let me present you: Adachi-ku, the northeastern tokyo ward with a shitty reputation. Japanese definitely will exaggerate when asked about Adachi claiming, it’s dangerous neighboorhood and to be careful but believe me it’s perfectly safe, whatever the crime rate is in Adachi-ku it’s a complete joke compared to pretty much any city in Europe or America. The typical resident in Adachi is either working class, unemployed or a struggling single mom who can’t afford better.
However, the greatest risk of actually being a victim of a crime is not in any suburb but the city where stuff goes down. Roppongi actually do have higher than average crime rate but that’s also because it’s jam packed with people, bars and clubs. Of course, shady stuff is going to go on there.
I wrote earlier an article about Ikebukuro being awesome. The thing is Ikebukuro used to be a lot more rough in the past. And you still see more than usual taboo establishments(adult stuff) in this part of the city than others. But from safety perspective, it’s completely fine neighboorhood to work and live in.
To sum it up, Tokyo is so safe there isn’t really any part of the city that you need to be worried about someone jumping on you. Even in the nightlife areas drunk people are remarkably non-violent in Japan. You will be annoyed by the drunk salarymen shouting but that’s about it.