Flying NRT-EWR-YYZ, on one e-ticket, your bag should still be tagged at NRT to YYZ. You will simply retrieve your bag before Customs at EWR,carry it through Customs and then drop it with AC just post Customs. You will not have to wait or recheck, simply drop it because it is already tagged.
You may have experienced an International-to-International (I-T-I) pilot at ORD in which bags arriving from outside the US and checked to another destination outside the US are not routinely inspected in the passenger's presence. Thus, you won't see the bag after it is checked at NRT until Customs at YYZ. The only two US airports with full-time I-T-I are IAH and DFW and bags subject to I-T-I carry a special tag which you would have seen applied at NRT.