FreeCAD, SketchUp. You could even do it in Blender.
Yes probably all mentioned 3D programs.
However, in this case - a box that is meant to hold a pcb card with hard fixed dimensions, I'l advocate for FreeCAD over Blender (but I may not be complete unbiased here as I've spend time learning the basic of FreeCAD but not Blender).
In Freecad, I'd looking for a workflow (oversimplified) like this:
- Make a body (term fora object with a clear 3D boundary) with known dimensions - not necessarily a true copy with all details but must consist of pcb board, screw holes and all objects that the box must be formed around.
- Use binders so that you can relate to this dimensions when you construct the box and lid.