I am no expert myslef, but I believe that Master equation analyses of Bose-Einstein condensation have indeed been employed in the past. E.g. in the works of Gardiner, Zoller and co-workes (for example, "Quantum kinetic theory III", PRA 58, 536 (1998) ), and of Scully, Zubairy and co-workers (for example, "Condensation of N bosons II", PRA 61, 023609 (2000) ). The above two papers include derivations of the master equations they study.
A nice recent application of this approach was to study what happens to condensation in a non-equilibrium steady state (answer: several condensates may form!), see Vorberg et. al, PRL 111, 240405 (2013).