Safety in Tokyo and Ueda

Roppongi is an upscale and quite good neighborhood otherwise; just be careful when it comes to night life.

On the other hand, try to avoid the red light districts, such as Kabuki-cho and Shinjuku 2-chome. If you go, don't engage anyone and especially don't partake in "special" activities. Most likely you won't get mugged or anything, but do be careful.

Also, avoid missionaries and far-right protesters (i.e. people shouting with loudspeakers and who apparently are not campaigning politicians), as they occasionally pop up at the street. They won't do any harm to you, but conflict is more likely around them (plus they're really annoying).

As for Ueda, I have not been there but the city looks like an idyllic city in the mountains (but not middle of nowhere either). Therefore I would be even less concerned with safety there. Of course, if you do hike, pay attention to geological failure and animals as usual (and, in the winter, snowstorms). According to the comments, this basically means stay on paved roads.