Has the second law of thermodynamics been repealed?

Hahah, life certainly flies in the face of the 2nd law, as do many of our creations.

No, this is using thermal energy from the environment and converting it to electrical energy. The ripples in the graphene sheet come from thermal energy in the environment.

To answer the Title's question - No.

It does rather sounds like it is violating the laws of thermodynamics, unless it is using temperature gradients like a thermoelectric cell. If it just sits there in a uniform temperature bath and harvests energy, that sounds very much like a violation of the laws of thermodynamics.

It's not violating any laws of quantum mechanics or thermodynamics.
Energy is all around us, we are literally made of it.
They probably had to have some very sophisticated device and or specific conditions to make it work, that will be the snag.

So how sure were the researchers that the energy wasn’t being pumped into the graphine by the tunneling electron microscope? The excitation level of an atom (or several atoms) may have been raised by the process of observing it.

I would have to see this scaled up to the output of a button cell battery to find it useful or would it be huge by comparison?

I think the second law of thermodynamics doesn't apply at this scale. The graphene, sort of like Maxwell's demon is only responding to the most energetic collisions that are happening from particles at the tip of the high end of the bell curve. Because it's managing to respond to individual collisions, the averaging necessary for the macro scale thermodynamic law to work doesn't occur. Quantum phenomena follow different rules. Another example is how microwaves tuned to the rotational quantum number of water pass right through styrofoam (because it can't pick up energy in exactly that size chunk), but the heat from the rotating water molecules gets trapped inside the cup.

We already have self-winding automatics & solar collectors that can power wrist watches practically indefinitely. I also have a Seiko kinetic which is essentially a mini generator powering the quartz. Micro harvesters & power efficient circuits are the future. An FM harvester is also cheap & simple, there's another option. For example, my Casio "wave ceptor" has an FM receiver to self-adjust to an atomic clock each night at 1am or so, to me it should be using that as an energy source as well!