You can export Shopify Variant Metafields with EZ Exporter by simply specifying the namespace and key.

In the Data Settings, under the "Metafields" section, enter the namespace and key of the specific metafields you want exported and they will be exported in separate columns.  You can specify your own custom column name here as well.

Example:

Variant metafields can be included in a Product, Order, or Draft Order export.