In terms of petty crime and thuggery in the streets no. The yakuza aren't good people, but having that structure means low level thugs have to be a part of the hierarchy and follow some rules. Rather than exterminating them, the Japanese police allowed them to exist in a symbiotic relationship, where they were kept in check with constant surveillance (guys on the inside), and were used to keep small-time gangs at manageable levels. Only the egregious examples of bosses openly committing violent crime or extortion were targeted. I do think that contributed to the famous safety of Japanese streets. We see the opposite in America where individual incidents of violent crime and theft started going up in Chicago and Las Vegas not long after major mafia crackdowns. As bad as they were, the mob wouldn't have allowed joggers jogging through their neighborhoods.

If we're talking NYC and how the mob was entangled in all construction and garbage collection and shit, yeah getting them out of the business was a big boon for business. They're still around in unions and some smaller businesses though, but not powerful enough to threaten street thugs.