^(Note: these are all books I've read and can recommend from experience.)

David Brin's Sundiver is a detective mystery. Likewise his Existence is a mystery about a recently discovered artifact, though its presentation with multiple perspectives lacks the singular detective tone of Sundiver. It's not as much of a mystery/thriller more of a mystery/adventure. It is also one of the overall best science fiction novels I've ever read; the writing is top notch, the characters superbly lifelike, the tone excellent, and the overall reading experience enjoyable and filled with a realistic optimism.

Gregory Benford's Artifact is an investigative mystery about a strange artifact. His Timescape is about a strange phenomenon.

Jack McDevitt's The Engines of God is an investigative mystery about a strange artifact.

Asimov's The End of Eternity is a classic mystery/thriller.

Alastair Reynolds' The Prefect and Chasm City are both standalone detective mysteries. His Revelation Space is similar, but does not have the same classic mystery tone.

Greg Bear's Queen of Angels and Slant are both standalone detective mysteries.

I seem to recall the Second Foundation (Foundation's Fear, Foundation and Chaos, Foundation's Triumph) trilogy by Greg Bear, Gregory Benford, and David Brin having some mystery aspects. I think one of them at least is a detective mystery, but I can't remember which right now.

Dan Simmons' Ilium/Olympos is a sort of detective mystery, but its tone is much more action/adventure despite the protagonist's undertakings to determine what in the world is going on.

Joan D. Vinge's Cat Trilogy (Psion, Catspaw, and Dreamfall) are detective mysteries.

Julian May's Perseus Spur is a detective mystery. It's pretty light-hearted and a lot of fun to read. Something you would pick up at an airport bookstore and not be at all disappointed with. I can't speak for the other two books in the trilogy, haven't read them yet. Just ordered them off Amazon for $4 a piece.

I could go on, but I think that should keep you busy for a while.

 

^(Edited to clarify the tone of some suggestions. Some are more traditional mystery/thriller, while others are more adventure/mystery, more alike to Indiana Jones than a noir detective.)

I am a big fan of Alastair Reynolds' Chasm City because it has a pretty good twist.

I'd like to give you an unbiased view of his books but I'm afraid when it comes Alastair Reynolds I suffer from a blatent case of fanboyism; he's the only good scifi writer novelist us Welsh have (nearly insulted all the Doctor Who fans there), it still amazes me how many great scifi writers Scotland produces in comparison.

I believe his characterisation improves, this was after all his first novel.

His biggest strength IMHO is his worldbuilding, I can't get enough of his Revelation Space universe. His second novel set in the Revelation Space universe (although can be read as stand-alone) Chasm City is my favourite as it started me on my journey through his universe and generally got me hooked on all his writing.

The last one The Prefect set before the melding plague was also excellent, I'm hoping he writes a few more over this time period after finishing 'Poseidons Children'.

TLDR; I'd recommend to keep on reading, you will be rewarded.

Try Chasm City by Alastair Reynolds. First of all, probably my favourite space epic of all time, the Revelation Space story arc is amazing and I love his focus on technology and space travel/combat. That said, Chasm City is more of a self-contained story that takes place primarily around a particular planet, and is one of the best twisty narratives I've had the pleasure of reading.

Specifically, Chasm City itself was a "golden age" style metropolis of kilometre-high skyscrapers and technology before a nano-plague took hold and transformed everything into a grotesque caricature of what it was. The city as it is "now" consists of the upper echelons existing in their now-dampened utopia while the slums far below have fallen to the poor and criminal.

...it's about time I read it again.

Here's a little bit of reference fiction for you:

Ship of Fools by Richard Paul Russo

• takes place on a generation ship. There are distinct upper and lower classes based on heritage. The original purpose of the mission has long been forgotten and the records been destroyed in revolutions past. An attempted mutiny takes place and is shutdown by the ruling party which elevates their position since preventing mutinities is the primary concern of the aristocracy. Lots of abandoned sections of the ship since the population is less large and less resourced than in generations past.
  
  Chasm City by Alistair Reynolds
  
  
• Half of the book involves flashbacks to a character's experience of being the last group of a 3-generation genship flight. A fleet of genships are sent on an interstellar migration. The fleet devolves into extreme prejudices, military rule, political intrigue, and activities contrary to the purpose of the mission: safely transporting their frozen human cargo to the target settlement planet. The hatred's developed during the flight transform into centuries-long warfare after the planet has been settled. Funnily enough, the settler's became oddity's in the human space world because sub-FTL flight is developed soon after they departed earth and the rest of the stars were settled with more sane people who could make the trip in a single lifetime.
  
  Analogue: A Hate Story
  
  
• An interactive fiction game where your job is to reconstruct what happened on a derelict generation ship. You learn that the idiotic descendants of the original ship crew have long forgotten what the ship was for, that they are even on a ship, and all the skills necessary to operate and maintain the ship. However, the root access for the ship's computer is owned by the emperor. The people mimic a Korean Josun Dynasty society. An inhabitant of a sleep pod is awakened from a much earlier generation and is bewildered by what's become of the ship. She's also the only one that knows anything about the ship's system. Also, there's a ship AI. The story ends with everyone on the ship being spaced and suffocated.
  
  
  Honestly, I think the best potential for a generation ship game is trying to keep things from devolving into chaos, barbarism, totalitarianism and cannibalism. Of course, if you actually make it to your destination, did you manage to retain the skills and resources necessary to survive or actually accomplish the mission objective when you get there?
  
  Maybe you could have a partial win to the game if your crew completely dies out, but you were able to make an AI to complete part of the objectives when you arrive at your destination. So, it would be a score-based game, trying to see how much achievements you can make or how high a score you can accomplish.
  
  Again, I'm curious what your take is on this game setting.
  
  
  Edit:
  
  Thought of one more.
  
  Passages Series by localroger.
  
  
• The universe and human's are controlled and ruled by AI's and AI ships. I can't remember but in one of the stories, an AI wants to carry people across space and he requires them to meet a certain societal model before he will carry them. So, a cult is formed with very rigid social rules and requirements. After several generations, the cult is ready and he takes them through space. After many many generations, it's a sort of religious village existence, trying to find and take care of any discontents and dissidents before they cause trouble. Finally they arrive at their destination and they parachute to the planet and start a colony.