Hi Matt - For plywood, I prefer rabbet or locking rabbets. The rabbet shown will show only about half the edge. If you have room inside the box you can miter the corner and use a corner block (shown in red at 1/2" thickness) with glue and short screws or brads. Screws and brads just hold it till the glue sets up and reinforces the corner. A lot depends on how large the box is and how much weight it is expected to handle.
I also like to use Gorilla Glue (polyurethane, the foamy stuff) on plywood as it seems to hold better on end grain.
What's the best way to do this? Glue and nails?