The problem with the 1st option; buying a full case, means your going to spend $500+ on the low-end with no guarantee that the wine box or crate will be included. Most of the time the case will be shipped in a cardboard box. The only way to ensure the wooden wine crate is included is by buying directly from the vineyard when you visit. Once you add travel expenses and the headaches of having to bring the wine back home the cost is prohibitive.
The first option is pricey but the 2nd option requires alot of your time. High-end wine retailers buy by the case and often have some wine boxes or crates in stock. They usually use the wine boxes and crates for decoration and/or wine storage racks, so it's unlikely you'll be able to pop in and take a few off they're hands inexpensively. A wine store sells wine not wine crates, so if you buy alot of bottles on a regular basis the manager or owner will be more willing to establish a relationship with you. Once that happens you may be able to get your hands on a few over time.
There are some downsides to this option though. Granted, you may get some wine crates for free (Although you bought alot of bottles, had extra travel costs and spent alot of your time) your going to get the wine crates or boxes that the wine store can't use or doesn't want. This means they're going to be full of stickers, staples, markings, nails and probably damages. Your going to need to spend even more of your time removing these things to make sure the box is looking it's best for your project.
Finally for the 3rd and last option you can buy them directly from a source such as www.winecratesandboxes.com where you simply purchase the amount of crates or boxes you want and their quickly delivered to your door. On top of that they come refurbished without any stickers, staples, nails etc. This means you don't have to deal with any of the prep work. You also have the option of buying them with lids, which is nearly impossible to find anywhere else.
Here's a listing of pages & links to buy wine crates from: