Noise in pentacene thin film transistors has been measured as a function of device thickness from well above the effective conduction channel thickness to only two conducting layers. Over the entire thickness range, the spectral noise form is 1/f, and the noise parameter varies inversely with gate voltage, confirming that the noise is due to mobility fluctuations, even in the thinnest films. Hooge's parameter varies as an inverse power-law with conductivity for all film thicknesses. The magnitude and transport characteristics of the spectral noise are well explained in terms of percolative effects arising from the grain boundary structure.