Look at the usual suppliers like All Electronics, Goldmine, MP Jones, Radio Shack, etc.
Note you can also make your own boxes from flat plastic stock. Get some acrylic or PVC and glue it together. PVC glue can be gotten at home centers and methylene chloride is the glue for acrylic. If you make nice smooth edges, acrylic can be glued quite successfully.
I got some tiny plastic boxes very much like the one you described at Mouser. They look so much better than any home-made thing I could make out of flat pieces!
It may be a little bit too big for your project but the mini-altoids tins are probably close to the size that you are looking for. Just line the inside with electrical tape to prevent the metal from shorting out your circuit.