Tristan Vick here.
In my research for U.S. Notaries, I found that Harris Lawfirms in Tokyo can do U.S. Notarization almost any day of the week. You simply need to book an appointment online.
Whereas the U.S. Embassy and Consulates only offer Notary services a couple days a week or less (and require the hassle of going through security).
Here’s the link to the Harris Lawfirms notary online appointment page if anyone is in need of an emergency notary.