Japan's consular network in the United States handles a short list of services well, and a good deal of what people come to it for is handled somewhere else entirely. These nineteen guides say which is which.
The two most searched questions in this whole subject are about visas, and for a U.S. passport holder travelling as a tourist the answer to both is that there is nothing to apply for.
The nineteen guides
Travelling to Japan
Japanese passport
Family register and civil status
Certificates the consulate issues
Nationality
What you can settle without going
You can check whether you need a visa at all, because most U.S. passport holders do not for stays under 90 days.
You can fill in Visit Japan Web before you fly, which covers immigration and customs.
You can apply for the eVISA online if your nationality is not visa-exempt.
You can order a koseki copy from your registered domicile in Japan by mail.
You can get an apostille for a U.S. document from the Secretary of State of the issuing state, not from a Japanese consulate.
You can register your address abroad through ORR net instead of at the counter.
You can download and fill in the passport application form before your appointment.
You can have the Certificate of Eligibility applied for in Japan by your sponsor.
You can check the office hours: most consular counters close at midday.
