Welcome aboard, Shannon!
If it's not near the coolant ports, it is indeed simply oxidization. The bad news is, it's a bit of a PITA to remove without pulling the manifold.
You were on the right track with the vinegar/water solution (don't use white wine vinegar but standard cheap vinegar), AND also use a brush (stronger than a toothbrush, but not aggressive like a steel wire brush). A black nylon bristle brush (or a brass bristle brush) should do it.
Realistically, unless you're detailing it for sale, it's not hurting anything, and sometimes you can do more harm than good since the solution will get on other components...
If it were mine, I'd pull the manifold (maybe when you replace injectors), glass-bead blast it, and clear-coat with clear gloss paint or clear powdercoat. But again, more invasive than necessary unless you're selling or showing.