I didn't think this could be done, but it can.
Porter airlines just started service between Toronto City Airport (YTZ) and Newark (EWR). My SO took a flight last night and he went through customs here in the States. (He told me he was surprised when he found himself at the gate and almost thought that he was going to bypass customs altogether!)
So those of you trying to get the work auth. stamp when you come in, this might be a way to do it. Obviously it's not JFK so there's no guarantee, but I guess one could ask for the stamp at Newark and see what happens.