"Warp core" is a somewhat nonsensical term. "Main reactor" or "matter/antimatter reactor" is more accurate.
Anyway, opinions differ, and the dialog from the show is somewhat contradictory. Some episodes seem to indicate that the nacelles themselves had self-contained reactors. Others seem to indicate that one or more reactors are located in the engineering hull. The latter is what I personally believe. The nacelles are just for warping space - power generation and fuel storage are the job of the secondary hull.
drew up the best damn 1701 cutaway I've ever seen. You can see the reactor located under the deck in the main engine room: