You would need to have an order in your Shopify store from which to create a shipping label. You could create a draft order with the customer information, and enter the item(s) as custom item(s), then mark it as paid. Once that is done you will be able to create a shipping label as with any other order. Just keep in mind that the information from any order created this way will flow into your Shopify store's metrics (sales, etc.) going forward.
Alternately, you can use other discount shipping platforms such as Stamps.com, Pirateship.com, ShipStation, EasyShip, Shippo, etc. for shipping orders that are not from Shopify. Some of these have no subscription or per-label fee, some have subscription fees, and some just have per-label fees, and the USPS/UPS rates are mostly comparable to those in Shopify Shipping.