It depends.
For used, you can stalk watchrecon.com.
For new, there are different Japanese vendors. The regulars are seiyajapan, chino watch and higuchi. The latter two are actual authorized dealers. You can also place an order from a different vendor through Rakuten.com - this is like the equivalent of Amazon marketplace in Japan. You do have to make sure the vendor you are interested in has good feedback though.
Edit - there is also ebay, though in my experience, the sellers tend to obtain the watch after you pay them. If their local shop is sold out, they give you a refund.