Don't forget that you have the BART transit system at the SFO airport to take you (easily) downtown. I did an overnighter to SFO a few years ago, and got on BART and went to a Courtyard by Marriott a block or two from Market street. It was an easy walk, and an enjoyable "extra" for the trip. If this idea appeals, look for your favorite hotels online, and the BART website.

One key is if they will let you check your baggage through to NGO (from BOS). If yes, then you can just pack a small carry-on with what you need overnight in SFO. If not, then you have some bags to lug around.

It used to not be a problem for an overnight connect, as long as it was "next flight out". Now though, sometimes they have a problem with a long connect, and want you to check your bag to the intermediate point, claim it, then recheck it, claiming "security." (Maybe this is a TSA rule?) Curious that they don't seem to trust being able to keep baggage that has been scanned by them to remain secure within their own system??

Another question is (if not an elite) and you must check to SFO: Will they charge you for your bagsm even though BOS>SFO is part of an international itinerary? I just looked at the baggage policy, and see nothing about that. If I remember correctly, that point used to be addressed previously.

With a name like TokyoKid, why go on to Nagoya? Shouldn't NRT be your destination?