[JSWolf]

Another answer is ....

Best Answer - Chosen by Asker
Here's the Book order:
Halo: Contact Harvest
Halo: The fall of Reach
Halo: The Flood
Halo: First Strike
Halo: Ghosts of Onyx

Game Order:
Halo 1 - 3

Chronological Order:

Halo: Contact Harvest
Halo: The fall of Reach
Halo 1/Halo: The Flood (the book takes place during the first game)
Halo: First Strike
Halo 2
Halo 3/Halo: Ghosts of Onyx (some parts of the book take place during halo 3)

This fits in with the list I posted other then it does not have The Cole Protocol listed.