^(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.)

The Chrysalids, The Kraken Wakes, - John Wyndham
Timescape Gregory Benford

Timescape won the Nebula and I recommend it too. It's hard SF if you can have such a thing with regard to time travel.
edit: I finished Courts of the Sun not too long ago and thought it was decent. I was dissapointed to come to the end only to find that it's supposed to be the first novel of a trilogy.

Years ago there was a book by science fiction writer/scientist Gregory Benford, Timescape about how the world food chain collapses because of these algae blooms fed by agricultural runoff.

Argh, thanks! I specifically checked this, and somehow the Letters part snuck in. Probably Timescape's fault.

I would suggest "Timescape" by Gregory Benford. link