The symbol seems due to Poincaré (1901, p. 456):
For brevity we will introduce the following symbol, by setting,
$$
\Delta\mathrm U -\mathrm K_0\frac{d^2\mathrm U}{dt^2}=\Box\mathrm U
$$
Here $\mathrm K_0=1\,/\,c^2$ (p. 336). It didn’t immediately catch on: it appears without comment in Poincaré’s (1906, p. 132) (cited by Wikipedia), but not in the book where Lorentz named it (1909, p. 17):
the operation $\Delta-\frac1{c^2}\frac{\partial^2}{\partial t^2}$ may be given the name of the Dalembertian (...) in commemoration of the fact that the mathematician d’Alembert was the first to solve a partial differential equation (...) which contains this operation, or rather the operation $\frac{\partial^2}{\partial x^2}-\frac1{c^2}\frac{\partial^2}{\partial t^2}$
In (1910, p. 175) Lewis (of photon fame) was still suggesting the notation
$$
\diamondsuit^2=
\frac{\partial^2}{\partial x_1^2} +
\frac{\partial^2}{\partial x_2^2} +
\frac{\partial^2}{\partial x_3^2} +
\frac{\partial^2}{\partial x_4^2}\qquad(x_4=ict),
$$
but Sommerfeld (1910, p. 661) and von Laue (1911, p. 71) chose again $\Box$ (pronounced “Delta”).
Note: Sommerfeld (ibid.) says the symbol was already introduced by Cauchy. This is repeated by Silberstein (1912, p. 805; 1914, p. 113), Bateman (1915, p. 6) and Pauli (1921, p. 607), but neither gives a citation. (Perhaps they mean this?)