You should be fine. Yes, you will have to show your AQ itinerary or locator number to the CO check-in agent in EWR. Any half-way competent agent will know how to interline your baggage. AQ is not my primary interisland resource, but I have had occasion to interline with them, and they were competent at this end. In one case, my bags made a 30 minute connection to ITO on AQ.

My only complaint with AQ's baggage arrangements is that every time I use them for interisland with HNL for a final destination, it seems to take them FOVEVER to cough up the bags onto the carousel. Mind you, I have only done that about four or five times, but it was like waiting for Christmas every time. On the upside, nearly every time I have come into ITO on AQ, my bags were already on the carousel by the time I walked down there.