I looked around for info on mineral-based pigments of the Northeast woodlands but couldn't find anything other than different colored clays. So, it looks like clay (mixed with water, plant oil, or tree sap) was the main thing used for painting wood with a color that wouldn't fade over time. And the only thing that I could find to make the paint job waterproof is walnut oil. Walnut oil is able to harden over time, like linseed oil. This is a very rare trait among the various other oils available in the Northeast.
You can also mix mineral pigments with animal-based fats like duck fat and bear fat. But these will smear and collect dirt unless you put them on in very light coats. This means the colors will be faint and not very noticeable. Fats are also not waterproof.
There is an art to painting with hot pitch, tar, asphaltum, and plant sugar type paints. This might have been done in the old days but I personally think it was very rare. I've tried this technique and it can get very messy really quick.