Easiest is to pre-plan so that there is space and supplies for the liquid in checked. I would wrap the bottle in bubble wrap and then place it between layers of clothes with nothing hard near it.

FYI - There is no such thing as "transit" in the USA. You will be entering the USA through all entry formalities, including Customs inspection, dropping your checked luggage back off with your carrier, proceeding through security checkpoint and then off to your NRT gate. Therefore, make sure that all of your docs are in order for USA entry, not just Japan, in case those are different.