Herkimer is a resource type that includes Amethyst, Calcite, Crystal (generic), Herkimer, Quartz, Pearl and Tellurite.
The various resources within this type are interchangeable for crafting common items. For crafting higher-quality blueprints, you will need to include two or more of these named resources, but not the generic resource.
Since the generic resources are all you can harvest at freeports and is all you will receive when you demolish structures, you will need to explore the game world in order to find many versions of resources of each type to build high-quality items and structures once you have looted some good blueprints.
You will harvest the most Herkimer with either a Metal Pick or a rhino, depending on your skills, the quality of your tool and the animal's stats.
You can find Herkimer in the regions linked in the chart below. Please store specific location information in the pages for the regions where you have found it. (How To Add a Region)