It depends on what you mean by "prominent". The biggest "family" is the Yamaguchi-guchi. They have around 40,000 members, and the government knows who they are because the family reports membership, like any good Japanese company. Will you ever see them? Maybe, but you probably won't know it. The Yakuza perform a very serious function in Japanese society in that organized crime squashes unorganized crime. What do I mean? The Yakuza do the usual prostitution, protection, etc that you find in the mafia. They are very involved in the "sin" trades. The Government turns a relatively blind eye to these activities for several reasons, but chief among them is that the Yakuza keep the streets safe. If some punk wants to rob people or purse-snatch, the police will go to the Yakuza bosses and demand an end to it. The Yakuza in turn, find the guy and either beat him to within and inch of his life, or recruit him.
I live in a town that used to have a well-known Yakuza faction. A couple of years ago, they got into a turf war with a nearby group that had split off. It was mostly about controlling sin trades, but there were other factors. Within a few blocks of my apartment, there was the group's HQ. It was attacked one night by gunfire and a bomb. No-one was hurt, and innocents were not targeted. However, the local citizenry voted to boot them out of town. They had to relocate, and it was a bit difficult because other towns also voted to not let them establish a new HQ. At any rate, we all knew where their building was, and who they were, and what they did. It's a strange relationship.
There are a couple of books that get into the history of the Gov't, Police, Yakuza triad relationship. They go into far more detail than I can here. Needless to say, it is an interesting situation, but as a tourist you'll never notice them unless you go to a strip club, soapland, buy drugs, and so on. Even then, you probably won't see them unless you refuse to pay, disrespect the girl, or something. So, depending on what you mean by "prominent," they play a prominent, but somewhat invisible role in Japanese society.
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