My rarest game is Genco's Big League from 1940. I've got no clue about production numbers. What I do know is that I've never heard about another person that owns one. Yet. http://www.ipdb.org/machine.cgi?id=259
For my more 'modern' games (the ones that have flippers), I'm not sure which one is the rarest. I've got a Night Moves cocktail pin by International Concepts (essentially a Gottlieb game, made under contract). Supposedly about 500 of these were made.
But I also recently acquired a Hot Fire Birds by German manufacturer NSM. I think this one is more rare than the Night Moves, but I'm not sure. I had personally never seen one before. Funny thing is that this game also has a Gottlieb link: the playfield was made by them: again, probably under contract. Two rare Gottliebs in disguises, so to speak.
Some pictures:
Big League
Night Moves
Hot Fire Birds backglass
Hot Fire Birds playfield