If you balance anything on a small point, that point will lie vertically underneath the center of gravity. Which means it lies on the resulting (vertical) line. You could mark the bottom contact point, and the top place where where that line crosses the object.
Change the orientation of the object, find the new balance point, and that will still be true. That creates a different line, because the contact point is different, and "vertical" is now in a different direction relative to points on the object.
The intersection of those two lines will be the COG.
You could add additional orientations, and get many lines, so you can more accurately estimate things.
I am, BTW, assuming that the object is rigid. I.E., that balancing it on the point doesn't change it's shape.
However, barring special cases like whitewater boats, which have to be made very sturdy for specialized reasons, and some other very small boats, balancing a ship on a small enough point to make useful estimations is likely to damage the ship. Maybe you could do it with a rubber raft, but it wouldn't be rigid.
There is, BTW, another complication, which makes my method approximate, especially for very tall ships. The weight of any element of the object depends (slightly) on the strength "gravity" at that point. Which to a first approximation depends on the distance from the center of the earth, and on the latitude (because "weight" includes the centrifugal force from the spin of the earth). (This is also the reason why the COG is not the same as the center of mass. I think engineers who design skyscrapers make a significant distinction between COG and COM, because the force of gravity varies. I don't know if any ships are tall enough for this effect to be significant.) And if you want to get really picky, you have to include tidal forces - i.e., at various tidal stages, your COG will be slightly different - but not enough to notice. My best guess is an approximation at any given ship orientation, altitude, and position on the earth will be good enough for all practical purposes at other ship orientations, altitudes and positions.
A more significant difference, for sailing craft, is that the shape and weight distribution of the ship depends on where the boom is currently located.
There is another way to estimate the COG, but it takes a lot of work. Create a scale model of the ship, using the same materials, and with the thicknesses of everything scaled to match. Ignoring the probably insignificant changes in the force of gravity I mentioned above, It's COG point will be the same as the corresponding COG point in the full scale ship. Since it is smaller, it might be strong enough to use my method.
But if you are good at computers it might be easier to create a 3D model of the ship in a computer. You create a fine mesh 3 dimensional grid of boxes that encompasses the ship. For each grid box, multiply the weight of the parts of the ship in that grid box by the x-position of that grid box. Sum those values together, and divide by the total weight. That will be the x-position of the COG. You can do the same for the y and z axis.
Technically what you are doing is an integral. I.E., the COG is the (3 dimensional) integral of (the density of the ship times the 3 dimensional vector positions), divided by the total weight. But if you understand that, you probably didn't need to ask this question.