We develop spectral theory for the generator of the $q$-Boson (stochastic) particle system. Our central result is a Plancherel type isomorphism theorem for this system. This theorem has various implications. It proves the completeness of the Bethe ansatz for the $q$-Boson generator and consequently enables us to solve the Kolmogorov forward and backward equations for general initial data. Owing to a Markov duality with $q$-TASEP ($q$-deformed totally asymmetric simple exclusion process), this leads to moment formulas which characterize the fixed time distribution of $q$-TASEP started from general initial conditions. The theorem also implies the biorthogonality of the left and right eigenfunctions. We consider limits of our $q$-Boson results to a discrete delta Bose gas considered previously by van Diejen, as well as to another discrete delta Bose gas that describes the evolution of moments of the semi-discrete stochastic heat equation (or equivalently, the O’Connell–Yor semi-discrete directed polymer partition function). A further limit takes us to the delta Bose gas which arises in studying moments of the stochastic heat equation/Kardar–Parisi–Zhang equation.