The rate of nucleation processes such as the freezing of a supercooled liquid or the condensation of supersaturated vapour is mainly determined by the height of the nucleation barrier and the diffusion coefficient for the motion across it. Here, we use a Bayesian inference algorithm for Markovian dynamics to extract simultaneously the free energy profile and the diffusion coefficient in the nucleation barrier region from short molecular dynamics trajectories. The specific example we study is the nucleation of vapour bubbles in liquid water under strongly negative pressures, for which we use the volume of the largest bubble as a reaction coordinate. Particular attention is paid to the effects of discretisation, the implementation of appropriate boundary conditions and the optimal selection of parameters. We find that the diffusivity is a linear function of the bubble volume over wide ranges of volumes and pressures, and is mainly determined by the viscosity of the liquid, as expected from the Rayleigh-Plesset theory for macroscopic bubble dynamics. The method is generally applicable to nucleation processes and yields important quantities for the estimation of nucleation rates in classical nucleation theory.