The inhomogeneous spin $q$-Whittaker polynomials are a family of symmetric polynomials which generalize the Macdonald polynomials at $t=0$. In this paper we prove that they are orthogonal with respect to a variant of the Sklyanin measure on the $n$ dimensional torus and as a result they form a basis of the space of symmetric polynomials in $n$ variables. Instrumental to the proof are inhomogeneous eigenrelations, which partially generalize those of Macdonald polynomials. We also consider several special cases of the inhomogeneous spin $q$-Whittaker polynomials, which include variants of symmetric Grothendieck polynomials or spin Whittaker functions.