For a better check through experience you need to do BOS-YYZ-NRT; on that flight you would not need to pick up your bags in YYZ and you would have a quick pass through the terminal w/o needing to exit security. However, if you add YYZ-YVR you must officially land in Canada and claim your bags take them through customs and re-check them to NRT and then go through domestic security. You will not need to see your bags again again until NRT.

If you have NRT-YVR-YYZ-BOS. You will need to pickup your bags both in YVR and YYZ, once to take them into Canada and then to take them in to the US. You still have to get your bags in YYZ if you go NRT-YYZ-BOS, but you can go directly from your arrival to US immigration.