Oh but you're asking two questions here!

My all time favorite slash piece, and I use that loosely because this is a series, is mirable_dictu's History of Atlantis, Part II. But I don't think it would be a very good first fic in the fandom because a) it's sad in a lot of places, and b) it's really quite long and you don't get to the fandom's favorite slash pairing for a while. I think it's beautiful and moving and hot in a lot of places and she gives us het pairings as well, but as an intro piece it might be a bit much. Given that my second and third favorites are a post death fic-- synecdochic's Freedom's Just Another Word...--and a really long multi-part AU--sheafrotherdon's Farm in Iowa--neither of those work either.

If I were trying to pimp the fandom, I'd go with two fics. I know you said one, but I'm generous that way. :)

Intersections by Kaneko. This one is a perfect first fic because you only have to have seen Rising to read it and yet it's so right for the characters that it still works after you've seen more eps.

Your Inevitable Unhappy Ending by Helen/helenish. I got pulled into the fandom by another fic of hers, but this is a fantastic introduction to both John and Rodney as a pairing and the Pegasus Galaxy as a whole.

And those are just my McKay/Sheppard picks. *facepalms*