It depends on whether you are comparing liquid nitrogen to liquid helium or gaseous nitrogen to gaseous helium. In general, the rules for viscosity are slightly different depending on which phase you are considering. For instance, in the liquid phase intermolecular interactions are important so that the viscosity tends to *decrease* as the temperature is raised. On the other hand, in the gas phase the intermolecular interactions don't seem to matter, and it is the velocity or degree of motion of the molecules that causes the viscosity of a gas to *increase* with increasing temperature. And there are situations that are sort of in between the two extremes where the two tendancies compete with each other more or less.
My guess is the confusion is arising by comparing apples to oranges. For instance, comparing the viscosities of liquid nitrogen to gaseous helium at a given temperature would be pointless as the two viscosities are in general related to two completely different sets of molecular phenomena. In one instance the viscosity of liquid nitrogen would be getting lower with increasing temperature and in the other case the viscosity of the gaseous helium would be getting higher as the temperature increased.
That's my answer anyways. Hope it helped.