Is there a way to re-order states in Craft Commerce?
Not at the moment, you would need to manually put the states at the top of your select box in the front-end. There is no harm if you have a duplicate select option in your form, so you could list the popular ones first, then list all of them.

We will look to add sorting of States in a future release of Craft Commerce. I have added it as a feature request and can follow progress there: https://github.com/craftcms/commerce/issues/1284