At the moment, it is my opinion that the top 4 rarest Pokemon (in order of rarity) are:
I’ve never seen a Lapras in the wild and have only caught them in 10km eggs. The theory that Lapras is the rarest Pokemon is also supported by Jeremy Lai (the guy that was the first to catch all the Pokemon), according to a new report I read.
Other rare Pokemon include Aerodactyl and a few others.
Since Gen 2 came out, I now think that the rarest Pokemon is Unown (one member on this forum mentioned that the had been a couple caught in Christchurch), followed by Porygon, then I guess the aforementioned.
Girafarig also seems rare to me, I’ve only seen (not caught) one.