The usual explanation for the molecular dipole moment of $\ce{NF3}$ being smaller than that of $\ce{NH3}$, despite the $\ce{N-F}$ dipole being stronger than the $\ce{N-H}$ dipole, is that influence of the lone electron pair on nitrogen is to oppose the net $\ce{N-F3}$ dipole, while enhancing that of $\ce{N-H3}$. See, for example, this good example.
What bothers me about this explanation is that when the $\ce{N-F}$ dipole is calculated (experimentally, I think), the effect of the electron pair on $\ce{N}$ is already factored in. Likewise for the calculation for $\ce{N-H}$.
Putting the question in terms of the language of the linked article:
[T]he lone pair's negative concentration will augment the polarity contribution from the polar bonds while for the $\ce{NF3}$, the lone pair's dipole would subtract from the dipole contributed by the NF bonds.
If the lone pair on $\ce{N}$ subtracts from the $\ce{N-F}$ bond in the molecule it must have had the same effect in the original diatomic dipole calculation. Likewise for $\ce{N-H}$.
If this is true, assuming identical $\ce{N-F}$ and $\ce{N-H}$ bond angles in $\ce{NF3}$ and $\ce{NH3}$, it seems that the vector calculation should still give a stronger dipole moment for $\ce{NF3}$. [Please regard this as a question!]
One thing that would lessen the molecular $\ce{NF3}$ dipole moment is a smaller $\ce{NF}$ bond angle (compared to $\ce{NH}$), which increases the lateral component of the dipole at the expense of the axial, making the (axial) resultant smaller. I think fluorine is larger than hydrogen and maybe this would tend to push the fluorine atoms out laterally, decreasing the resultant axial dipole. However I do not see this as an explanation in texts so I am guessing it is wrong.
My confusion is that the vector algebra doesn't seem to support the argument but there is probably something I am not taking into consideration.