What is the best way to rent in Tokyo?

I'm going to visit Tokyo in this july with tourist visa,but i don't know what is the best way to rent apartment there for 3 months as a tourist.Btw,student visa is probably better when renting,but is it so when your student visa is only 3 moths?

what is your nationality and where are you from ?
how have you got a permission to enter Japan ?
I believe the government closes the gate from almost all countries with some exceptions.
the exceptions are clues on international flights, Japanese nationality holders, and foreigners who got resident statuses (permanent, teijusha, etc. but, not student and not working) before April 2.

http://www.moj.go.jp/content/001318291.pdf

Russia.Embassy of Japan is working now,i'm going to apply for tourist visa,because my course is short-term.
I contacted them if they can give me visa or not due COVID-19,they said they can.

If your course is three months and you get three months on your visa (or the 90 days that normally applies under the visa waiver programme), then you don't need to get a student visa.
I had a friend spend three months in Shinjuku last year on a temporary visitor permit and they had no problems getting an apartment for the duration of their stay - it was small/functional, but pretty nice and reasonably priced for the location.
For renting, you're probably going to be looking at "monthly mansions" or similar. Alternatively there are foreigner friendly rental companies that offer short term space - either apartment or share house.

Have you applied with, and been accepted by, the language school you intend to attend? They should be able to help you with the visa (if you decide to go for the student one, in particular), and also with the accommodation. At least they should be able to recommend some places for you to stay in; the school might have some student accommodations of their own, or might be able to refer you to some landlord, or "monthly apartment/mansions."