As the title says, Im curious if the Nifs used for weapons and armours are compatible between Fallout New Vegas, and Fallout 3.

Anyone know if any alterations in the nifs have to be made?

While I have no experience working on .nifs, I can assure you that armours can be ported between Fallout New Vegas and Fallout 3. Weapons, however, will look broken when ported from Fallout 3 to New Vegas. I don't know if this is the case with all weapons though, since I only tried to port a revolver from Fallout 3 to New Vegas.