In Star Trek: Strange New Worlds IV, there is a TOS short story Tears for Eternity, that is set in the 523rd Century (about a new generation of Horta, sequel to The Devil in the Dark). However, (a) this perhaps isn't canon, and (b) I don't believe there's any reference to the Federation at that point.
In Star Trek: Strange New Worlds II, there is a TNG short story I Am Become Death, that is set in the 44th Century (about a future with many Datas, prequel to Brothers). However, (a) this probably isn't canon either, and (b) I haven't read this personally, so I don't know if the Data future has the federation, either.
In Living Witness (Voyager S4), an alternative Doctor is activated and heads off to the Alpha Quadrant in the 31st Century. I don't recall (but it's been a long time since I saw it) any mention of whether the Doctor knows that the Federation is/is not around at that time.
The ship from Future Tense (Enterprise S2) is from the 31st Century, and had human/Vulcan crew. I don't recall (also a long time since I've seen this) any mention of whether it is a Federation ship (probably not, since Enterprise don't know about the Federation at this stage).
In Future's End (Voyager S3) we see the U.S.S. Aeon from the 29th Century. This presumably is the Federation, and is canon - but the timeline is wiped by the events of that episode.
In Relativity (Voyager S5), a semi-sequel to Future's End, we see the inside of the Federation timeship Relativity, in the 29th century. This timeline was not erased by the episode's events.
In A Matter of Time (TNG S5) we see a time pod from the 26th Century (via the 20th). There's no indication of what the 26th Century is like, however.
In Crossroad (TOS novel) there's discussion of the Federation in the 26th Century:
Starfleet and the Federation are corrupt and controlled by a private company. A traveller from the future is trying to get rid of the Federation in Kirk's time to prevent this.
I'm not sure if this is canon or not, but it's probably the closest to addressing the future of the Federation itself, rather than just the future in general.
(As an aside: the novel is by Barbara Hambly, who has written many excellent non-Trek novels).