Perhaps a high level of crime for the Japanese but very safe for anyone used to living in western cities. The Nigerian muscle at the doors to some bars made me laugh when I was last there (some ten years back).
The Nigerian "muscle" aren't just bouncers. They are touts, pimps, drug dealers and shake down artists all wrapped into one.
But you are correct, Roppongi is generally safe compared to most places in the world. Two basic rules to avoid 99% of all problems:
1) Never go with a Nigerian to an establishment located in the second floor (or above) of a building. Safest bet is to just never go with a tout anywhere.
2) Never go to a second establishment suggested by a person (woman) that you just met that isn't Japanese. Particularly if they REALLY like you and they are (objectively) out of your league.
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Roppongi Hills is very nice, but I agree with your assessment of the rest of Roppongi. When ever I go back to visit I try to avoid Roppongi unless I am having dinner at the Oak Door.
The first choice piece of cow that place serves will be the first.
The bar, OTOH, can be the bees.