^(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.)

Vaguely reminiscent of Engines of God:

https://www.amazon.com/Engines-God-Jack-McDevitt/dp/0441002846

In which early exploration of nearby planetary systems by exoarchaeological teams reveals an entity of some kind that seems to target structures while leaving worlds wih only non-sentient life alone, and which may be headed toward our solar system.

Not a thriller but rather a neat series about the dangers and discoveries of interplanetary scientists. No assassins or other nonsense.

A brilliant stand alone scifi novel about academics trying to get as much information out of an alien dig site as they can before the entire planet is destroyed due to governmental necessity.

I found the book in a used bookstore in a wet, drippy, stinky basement in the enlisted soldier's club on Ramstein air force base. I was never so happy to find a good book in which to escape in all my life.

http://www.amazon.com/The-Engines-God-Jack-McDevitt/dp/0441002846

Oh man... I did not know this existed. I always thought Vall-henge was a nod to Engines of God

It sounds like a story by Jack McDevitt The Engines of God

http://www.amazon.com/Engines-God-Jack-McDevitt/dp/0441002846

so far down i doubt it will even get seen, but this is a book i thought would make an incredible movie since it came out

one of the most intriguing movies that could be made now that the technology exists to make it properly

Engines of God?

//edit: I'm not sure why I'm being downvoted, yes the alien monolith reference was meant to reference 2001: A Space Odyssey, but it's also the entire plot line behind the book I posted.