If you are staying in Tokyo for under a month, you’ll need to stay in a hostel or hotel. If you happen to be staying for a month or more, you can try a monthly apartment or live at a guest house. Be prepared in many cases for small rooms and cramped bathrooms. If you are considering an apartment versus a hotel, remember that the apartment may not have a western style bed. You may just have a futon on the floor. Be sure to check on this. Otherwise, hotels are pretty westernized.
For hotels, I suggest using http://travel.rakuten.com/ to search for available rooms. This will allow you to zoom in on your search depending on the price and specifications you require. I have used this search page to find a few hotels that were good for the price. However, you cannot know everything about the place before you go. I remember one place I booked had a shower I couldn’t even stand fully up in.
For a monthly apartment or guest house, go to http://sakura-house.com/ — they have the widest selection of prices and locations available. I have used them plenty of times in the past and they provide good support for foreigners travelling to Tokyo. They speak English very well and are easy to contact. However, in order to use them, you have to be staying for at least one month. You can always do partial months but the minimum period is 1 month.
The difference between an apartment and a guest house is usually that an apartment will have a private bathroom while in a guest house, you will share facilities with others. It is not entirely bad. I stayed in a Sakura House guest house once and the people there were generally friendly with a good mix of people from all around the world. We shared a bathroom, shower, kitchen and lounge area and had our own private rooms. Guest houses are much cheaper than apartments because of this.
Another option if you want to go cheaper is to stay at a hostel. The best way to find a hostel is to search online. Always look for sites that have user reviews such as http://www.hostels.com/tokyo/japan. User reviews are one of the best ways to avoid uncomfortable situations in cheaper places like these. Hostels vary wildly in what they provide and the options available for staying so make sure to do your research first.
If you want to go super cheap, you can just stay in an internet/manga cafe. I would only recommend this if you already know about these cafes and can speak some Japanese. Basically, you can get a good deal for one night of use with your own “private” room where you get a nice comfortable chair or padded area you can lie down on. You will have to check out the internet/manga cafes that are around to find the most comfortable one. Some even have showers available for use and free ice cream so make sure you get a good deal.
Additionally, you can stay directly in someone’s place by using the site http://airbnb.com/ — the prices and rooms vary but you can get a good stay in a nice apartment rather than a hotel. The rules for each place are usually determined by the owner.
You can also try staying in a capsule hotel where you get your own little capsule to sleep in. I stayed in one that came with a TV and radio along with a light inside. It was quite comfortable but can be a little more expensive than a hostel. There is a common shower room. These places are usually for people who have missed the last train home and are too drunk to wait it out. It’s probably the closest you can come to living in a human beehive.
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