Why do you need a 3D model? What boundary conditions do you have that are not axisymmetric?

Is the flow laminar or turbulent?  Nusselt Number is all about the boundary layer. Your mesh does not have small enough element thickness at the wall.  Have you divided the pipe into an entrance length where the velocity profile is developing and a downstream length where the flow is fully developed?  Are you computing the heat transfer coefficient in the fully developed region, or including the entrance length?