I've done the BOS-Japan trip more than a few times, and getting to KIX is a major chore. As jib71 says, you have to go via SFO or LAX, and that will easily add 2-3 hours to your trip compared to better connecting cities. It's best, by far, to fly in/out of NRT, and then make intra-Japan connections either by train or domestic flights.

I can't help you all that much with advice on economy. I'm sure that the service on ANA is about as good as you could get on any other carrier, and I understand that Air Canada isn't bad in econ. I've flown both between NRT and Boston, and AC's connection in Toronto isn't bad. On the way back, it gives you the longest amount of time in Tokyo -- the flight leaves NRT around 5.30pm and you still make a decent connection into BOS. Plus, you'll clear customs/immigration in Toronto, so you won't have that extra hold-up when you finally arrive in Boston.