If someone in Japan sends me tomato seeds through the mail, will the
post office or customs confiscate the package?

Assuming you are in the US.

from the US Customs & Border Protection - Bringing Agricultural
Products Into the United States
http://www.cbp.gov/xp/cgov/travel/clearing_goods/agri_prod_inus.xml

"ANY plant parts intended for growing (propagative) require a
phytosanitary certificate in advance."

application for a phytosanitary certificate can be found here
http://www.aphis.usda.gov/ppq/forms/ppqform587.pdf

I ahve looked at the sites given, but the seem a little ambiguious
about seeds. Plants or anything with roots seem to be forbidden or
regulated, but I would like to find a fairly definitive statement
about seeds in particular.

Seeds are a plant part intended for growing (propagative) use, which
as stated in the quote require a phytosanitary certificate.
The first item listed in the Plant Parts column of the certificate
application form is "seeds".

From the International Seed Exchange website, "It is illegal to import
seeds into the USA without a Phytosanitary Certificate".

It seems that you have answered my question. What do I do next?

If you wish to import them you need to download, complete and submit
the application for a phytosanitary certificate from
http://www.aphis.usda.gov/ppq/forms/ppqform587.pdf
The application can be submitted by fax of mail. The phone number for
enquiries is 1-877-770-5990.