1. Stay in a share house, or rent an apartment - it’s cheaper than you might think.
When Janez and I were planning our trip to Japan, one of our biggest worries was the accommodation. We have heard that the hotels were super expensive, so that was out of question, but the hostels didn’t seem like a good idea either...I mean, we were about to LIVE there for a month - there was no way we were going to leave our luggage (and money) in a room with other people, and we did need some storage space.
Ultimately, we decided to rent a room with Sakura House, which turned out to be a really good decision. There are many companies in Japan that rent apartments, rooms and dorms to foreigners, and the prices are actually very reasonable, especially if you are traveling with someone who you are willing to share the room with. Say, the two of us had to pay 700 euros for a one-month-stay, which was only 350 euros per person for a one month stay in the very center of Tokyo. Trust me, that’s an incredible deal.
Here, you may want to take a look at some of these pages:
http://www.sakura-house.com/en
https://www.oakhouse.jp/eng/
http://www.borderless-house.com/jp/
https://www.realestate.co.jp/en/rent
With this one, you may want to be a bit careful when specifying the search terms...I found that “Residence Tokyo” apartments suit my needs the best, for example, with the whole no guarantor and such.
There is always the AirBnB option to explore too, but as far as I remember the prices there were noticeably higher than the prices of these share houses. It is still worth checking out, though :)