For the wood boxes, if I'm imagining the same thing, they are generally used as a box to hold something more valuable, like a nice cup. When you buy the cup, you get the box. A Google search for "Japanese wood gift box" might get you some hits. My impression is that you can't just buy the box, unless you buy several because you want to package your products nicely. As for sake cups, there are zillions of designs from glass, to fine china, to rough pottery, to wood boxes. Any department store should have a wide variety.