Cybervision64 is faster, it has also got an automatic passthrough for a scandoubler. CV64 is only for Z3 bus.
CyberVision64 3D is slower, it has an optional scandoubler wich is hard to track down. The card wont automatic switch between CGFX and native GFX without the scandoubler. The scandoubler is not 24-bit so it wont show complete spectrum of AGA colors. Picture quality is said to be worse with CV643D and scandoubler module than CV64. CV643d is for Z3 and Z2 bus. But still, its a nice GFX board.
CyberVision64 3D has built in 3D functions, but I can only think of Tornado 3D and Descent that uses the Virgie functions (anymore programs?).