In order to analyze incompressible and laminar fluid flows in presence of geometric uncertainties on the boundaries, the Non-Intrusive Polynomial Chaos method is employed, which allows the use of a deterministic fluid dynamic solver. The quantification of the fluid flow uncertainties is based on a set of deterministic response evaluations, which are obtained through a Radial Basis Function-generated Finite Differences meshless method. The use of such deterministic solver represents the key point of the analysis, thanks to the computational efficiency and similar accuracy over the traditional mesh-based numerical methods. The validation of the proposed approach is carried out through the solution of the flow past a 2D spinning cylinder near a moving wall and the flow over a backward-facing step, in presence of stochastic geometries. The applicability to practical problems is demonstrated through the investigation of geometric uncertainty effects on the forced convection of Al2O3-water nanofluid laminar flow in a grooved microchannel.