They will work and are officially cross-compatible, but the concavity of the pucks shipped with the S4 is slightly deeper, despite there being no official acknowledgment via a different model number or such.
As a result, the newer pucks can physically mate with the S4 and previous versions equally well, while an S4 won't mate completely flush with the S3 and older pucks.
I noticed this during an S4/S3 swap, during which we tried to figure out which parts to Lego and keep. The bands are fine, but the pucks are ever so slightly different. However, I think this would only make a practical difference if an older puck is mounted vertically in a stand or something, and it has less magnetic force to hold an S4 in place, but we didn't test that scenario.