If that is the case, something is wrong.
Typically Geometry 3D results in a ~50%-60% performance decrease compared to playing on your monitor since everything has to be rendered twice to create the stereo 3D effect. For a game as old as Fallout 3/NV that still results in a very smooth frame rate normally though.
Please double check whether you maybe have any mods installed that have an high impact on performance. If so, please remove them. Try without any mods first and then add your mods back one by one to find the one(s) that affect performance.
If that does not help, you should consider switching to Z3D in the vorpX menu. Doesn’t look as good, but has a much smaller impact on performance.
You can find additional information regarding game performance in the “Performance Optimization” section of the vorpX help.