Just wondering, is Japan a safe country to go to if you're going by yourself and you want to check out the night life? Are there any threats such as Yakuza, etc.

Yea,it's safe but I think there is a Yakuza but if you've seen enough movies and know a lot about the culture you will recognize who to stay away from

Even compared to small towns in the USA the crime rates in the most crime ridden city (Osaka) in japan the crime rates are lower than those in the small towns. So yes Japan is very safe as long as you avoid Yakuza (tatoos, cut fingertips, etc.)