When I called VAC NY at 646-741-0130 they said NY Consulate is not accepting passports directly anymore (since end of June, 2014). VAC NY or LA is the only way (at least for the time being) to get visa stamped in your passport if you are applying in the US.
Unless are you trying to save on the USD 34.10 VAC fee to process the visa stamping, I don't see any reason why you would risk sending your passport directly to the Consulate. If they return the passport to you and you have to send it to VAC anyway, it would only delay the whole process and wasted postage.
Also see this thread:
www.canadavisa.com/canada-immigration-discussion-board/can-i-avoid-using-the-vac-new-york-t229896.0.html
