Mode coupling due to scattering by weak random inhomogeneities in waveguides leads to loss of coherence of wave fields at long distances of propagation. This in turn leads to serious deterioration of coherent source localization methods, such as matched field. We study with analysis and numerical simulations how such deterioration occurs, and introduce a novel incoherent approach for long range source localization in random waveguides. It is based on a special form of transport theory for the incoherent fluctuations of the wave field. We study theoretically the statistical stability of the method and illustrate its performance with numerical simulations. We also show how it can be used to estimate the correlation function of the random fluctuations of the wave speed.