You can add the options ViewProjection, ViewPoint, and ViewVertical to make it appear as if it isometric:
Show[PlanePartitionDiagram[{{3, 3, 2, 1}, {0, 3, 2, 1}, {0, 3, 2, 1}, {0, 0, 0, 1}}], ViewProjection -> "Orthographic", ViewPoint -> {1, 1, 1}, ViewVertical -> {0, 0, 1} ] (should work with 11.2 and up).
