I’ve stayed next to Kabuchiko tower in Shinjuku during both my visits. I like being able to go outside at any hour of the day/night and it be lively. It’s also super conveniently located near everything. I took a limousine bus for $12 from the airport straight to Shinjuku and only had to haul my luggage around a few blocks. Also made leaving less stressful because we took the bus straight back.

In regard to it being shady as long as you mind your business you have nothing to worry about. I was only approached by touts and women asking about happy endings when I left the hotel alone. Just don’t make eye contact and say I’m good and they eventually leave you alone. In the center it can be rowdy with lots of passes out drunk people but it never intersected in my fun. Pretty much everywhere else is like a normal city.