From an interview with Valve Software's Chet Faliszek from Beefjack.com:
With regards to the co-op campaign, how does it fit in the Portal universe?
Chet Faliszek: It has its own separate story, with its own characters, and takes place after the single-player game. GLaDOS has a little thing for you to do, and I'll say no more to avoid spoilers! The story in co-op really has to step back a little bit because you need room for people to breathe and talk. They have their own story that's competing against it, you know? They won't go: "Remember when I was playing P-Body and you were Atlas and I pulled the light-bridge out from underneath you?" They're going to say: "Hey, remember when I pulled the light-bridge out from underneath you, and you fell off into the goo?" There's more of a personal story that comes from that.
Of course, no one's quite sure how the overall Portal 2 story will be woven into Half-Life, but there is some speculation (among a few random gamers that I've talked to) that part of the reason we haven't heard anything about Half-Life 3 at all is because events in Portal 2 will heavily affect the Half-Life universe. I'm starting to get a totally speculative hunch that we'll be hearing about Half-Life 3 soon after Portal 2 is on shelves. (Wishful thinking?)
Related: Valve Plans to Bridge Portal and Portal 2 With a Surprise, Keep Gordon Freeman Out Of It [Kotaku]