We develop methods for calculating the zero-frequency noise for quantum shuttles, i.e., nanoelectromechanical devices where the mechanical motion is quantized. As a model system we consider a three-dot array, where the internal electronic coherence both complicates and enriches the physics. Two different formulations are presented: (i) quantum regression theorem and (ii) the counting variable approach. It is demonstrated, both analytically and numerically, that the two formulations yield identical results, when the conditions of their respective applicability are fulfilled. We describe the results of extensive numerical calculations for current and current noise (Fano factor), based on a solution of a Markovian generalized master equation. The results for the current' and noise are further analyzed in terms of Wigner functions, which help to distinguish different transport regimes (in particular, shuttling versus cotunneling). In the case of weak interdot coupling, the electron transport proceeds via sequential tunneling between neighboring dots. A simple rate equation with the rates calculated analytically from the P(E) theory is developed and shown to agree with the full numerics.