Just use the equations that you have twice, but the second time swap in z for y.
That is, calculate the centroids of the two projections, one onto the x-y plane, and the other onto the x-z plane. The centroids of the projections will be projections of the actual centroid, so the answer will be the x, y, and z values you find from these two calculations.
Stated more explicitly: If your points are (x1, y1, z1), (x2, y2, z2),... , to get the x-y centroid, (Cx, Cy), do a calculation using (x1, y1), (x2, y2),... and to get the x-z centroid, (Cx, Cz) use the points (x1, z1), (x2, z2),.... -- just do the second calculation with your same 2D formula, treating the z values as the y in the equation. Then your 3D centroid will be (Cx, Cy, Cz). This will work as long as your surface is flat and isn't parallel to the x-y, x-z, or y-z planes (but if it is parallel it's just the 2D equation).