I actually read them in this order:
Ghosts of Onyx
Fall of Reach
First Strike
Contact Harvest
Cole Protocol
(Evolutions)
I didn't read The Flood because it literally just retells Halo CE. You can read Cole Protocol, Contact Harvest, or Ghosts of Onyx in any order, but it should definitely go Fall of Reach -> First Strike since they're kind of in the same direct story arc.
My favorite one though is Fall of Reach, then Ghosts of Onyx.