Spoilers below.
In the homebrew setting my Kingmaker is set in, elvish society is a gerontocracy - the oldest family member rules. And elves are descended from fey, the most powerful of which are immortal. Recent events in the last century or so have driven many powerful fey to come out of seclusion and re-enter the world. Nyrissa's plot is tied into this - and as it turns out, she happens to be the great-great-great-great-great-great- (etc.) grandmother to a large portion of the modern-day elvish settlement. While she rarely deigns to walk among them directly, I'm planning to have her directing their actions behind the scenes and influencing their politics and military actions.
I'm not sure yet how large the settlement/community will be, nor the exact effect it will have on the party, but I'm looking for a place to insert them into the game. Where would be a good place and time to involve this group, which will be antagonistic to any players or nations opposing Nyrissa's plans?
I might also tie this group in with an idea I had a few months ago for a clan of werewolf elves who prey on nearby human settlements until one of them accidentally infects a human barbarian who proves too strong for them to hunt down. They attempt to hire the players to put an end to the "dangerous werewolf" until the PCs discover the elves' true nature, and potentially ally with or cure the human werewolf, who just wants to return to normal. (As opposed to the elves, who just want to hunt humans for sport.)
Somewhere in the Greenwood would be fairly obvious, maybe too obvious ("Elves! In! Trees!") I like the idea of Lake Silverstep -- not nearly enough was done with the mountains in book 3, in my opinion. Putting them in the swamps (instead of the bog-striders) would be another possibility.
A great deal depends on when you want the PCs to encounter this place, and how tough you want the encounter to be.
There's a lot of space north of Pitax for an elven community, too, if you're planning to wait till near the end.
I figured you could put one between Pitax and the kingdom that the players will build, or somewhere in the mountains near Varnhold. Nobody expects mountain elves!