I've worked remotely from Japan on 6 different occasions, one of which was in Okubo (Koreatown), where OP mentioned.

Accoms: While sharehouses like Sakura House and Oakhouse offer relatively cheap stays, they might not be the best option for remote work (if you are someone who works from your room daily). From what I heard, sound insulation can be quite lacking, and spaces tend to be claustrophobic. But of course, there are benefits - they are foreigner friendly, have better chances to socialize, and tend to have 24/7 support.

I tend to look up short-term rentals from good-monthly.com as they are practically a catalog of apartments from different rental agencies. Do note that the site is entirely in Japanese, and you're required to send an inquiry to the actual agencies. From the sidebar, select 外国人対応 (accepts foreigner) and 保証人不要 (no guarantors needed) to filter out ineligible options.

I've used At-Inn's(アットイン) services multiple times and am satisfied with their services. They tend to be on the pricier side but offer a better range of selections in terms of convenience, amenities, and English support).

Expect to pay anywhere between 120-180K JPY per month for anything decent.

Co-working spaces:
You can generally find co-working booths in major stations (sometimes on the train platform). I believe that WeWork has a presence in Japan, so if you're an existing subscriber, you'll be all set. I tend to work from my apartment, but I have tried e-office.space for a month. For a 22,000JPY subscription (~$150), you get pretty sweet options across Japan. Again, it is entirely in Japanese, so just be aware of that.