It seems to be related to this: http://www.nexusmods.com/newvegas/mods/34690/?
At least it improved some (still a bit choppy) when I followed the instructions there and added the following to the Controls section of Fallout_default.ini
fForegroundMouseAccelBase=0
fForegroundMouseAccelTop=0
fForegroundMouseBase=0
fForegroundMouseMult=0
If anyone knows of anything that can further improve the mouse choppiness, it'd be appreciated.