There's a lot of places that fit that description.
But rent in Japan varies greatly depending on location within Tokyo, distance from train station, age of building, included fixtures, etc. There's specific formulas used to determined an apartment's worth.
So you need to know what type of commute suits you (how far to the train, how many changeovers), how much space you need, etc.
You also need to know whether or not your company will pay for the deposit and key money. (a total of 4-6 times the monthly rent: so for a 250,000 apartment you will need up to 1,500,000 just to get the key).
A 10 minute walk to the station is considered good/close.
If you're concerned about earthquakes, building standards, etc. you should look for a building built within the last 5-10 years. Before the Kobe earthquake, building standards really only existed in theory.
If you're someone that can't stand the idea of living in a small studio (imagine smaller than New York midtown studios), then you should look to have at least 50m2 for your living space.
You also need to know that Japanese can and will flat out refuse to rent to you simply because you are a foreigner. Japan's Xenophobia is most felt during the apartment hunt experience. It can be a depressing and humiliating experience for some so, if you don't speak Japanese, it's best (almost mandatory) to have a Japanese person that can help you through the experience.
All that said, I personally recommend the area between West Shinjuku and Hatsudai.
West Shinjuku is quite expensive but there are some gems to be found. There's not too much there but it's quite, clean, and pretty at night. Hatsudai is the neighborhood immediately to the west of West Shinjuku. Everything is always walking distance. Yoyogi Park, Opera City, Shinjuku station, the Shibuya area, etc. Every major neighborhood is almost a straight shot or 1 train changeover: Akihabara, Roppongi, Marunouchi, Chiyoda, etc. And, everything after that is a reasonable cab ride.
Again, there's a dozens of great neighborhoods in Tokyo, so you first have to figure out how the process works and what your needs are.
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