Thanks Mrj864, some of those sound interesting, and I didn't know about them. Probably the books about the president and staff are closest to the idea I have in mind. I'm thinking about books that aren't even directly about Starfleet. I'd like to see a political thriller or spy novel set in the Federation, something like that.
I that case then, you might like the
Section 31 books. I haven't read them but they are a 4 novel series about the super secret borderline illegal intelligence/ domestic security Federation agency. Seen in DS9 and the finale season of Enterprise.
If you like DS9 then there is the novel
A Stitch in Time about Garak, written by Andrew Robinson, the guy who played him on the show. About him trying to help rebuild Cardasia after the Dominion War while flashing back to his childhood and career as an agent in the Obsidian Order, the whole time writing the book like it is a letter to Dr Bashir. It is widely considered to be the best Star Trek novel ever. Hell, even if you aren’t a fan of DS9 I would suggest reading this book.
Your best bet for good political and espionage stories will be the DS9 re launch novels. Books like
The Left Hand of Destiny, about Chancellor Martok, Ambassador Worf and the Klingon Empire, written by J.G Hertzler (the guy who played him), I haven‘t read it but I heard it is good.
Then there is the epic three part
Terok Nor, that begins with first contact between Cardasia and Bajor and spans the 50 years of occupation and ends a couple of days before the first episode of DS9. It fits together with A stitch in Time really good. It parallels a lot of major events of the 20th century especially the Soviet occupation of Afghanistan in the 1980‘s.
The last one I will recommend is
The Never Ending Sacrifice about a Cardasian teenage boy raised by Bajorans who was sent back to Cardasia, against his will, to live with his people, who he hates, in the second season of DS9. And then tries to make a life for him self while trying to survive the events of the series. This also ties into A Stitch in Time.
I think that
A Stitch in Time and
Articles of The Federation are probably the best ones for you.