I've done this a lot from Boston. The JL nonstop is the best option; the seats are awful (sloping business class), but the service is very decent, and the time/aggravation saved by avoiding a plane change trumps any other option.

My second choice is Air Canada via Toronto. This is the shortest route to Tokyo if you're going to make a connection, the connection times are good, and I like AC's full-flat business seats (no F available).

To fly in F, the only viable choices would be ANA through either Chicago ro Dulles, or via the Atlantic. (Going through JFK would be madness; it's a serious pain to get from BOS to JFK, especially when using award tickets.) The problem with the Atlantic route is that it turns into a much longer trip, and you have back-to-back overnight flights. Also, if you use Lufthansa or BA, you're likely to be paying well over $1000 in fees. ANA's F is fine but then you still have the 2-hour aggravation of flying United to get to/from ORD or IAD.