Before I post my TOS list, I forgot to add
The Sky's the Limit to my previous list. It spans from before
Encounter at Farpoint to after
Nemesis. Also
The Brave and the Bold duology and
Tales of the Dominion War both contain TNG elements on the Enterprise-E. And I don't think anyone mentioned the TNG:
Double Helix series, some of which take place in this time period.
Here's my TOS list-
Pike Era:
Vulcan's Glory
Early Voyages
The Captain's Table: Where Sea Meets Sky
The Children of Kings
Burning Dreams
Pre-5-Year-Mission Era:
Inception
My Brother's Keeper: Republic
My Brother's Keeper: Constitution
The Five Year Mission Era:
My Brother's Keeper: Enterprise
Mere Anarchy: Things Fall Apart
The Captain's Table: War Dragons
Invasion: First Strike
Mere Anarchy: The Centre Cannot Hold
Day of Honor: Treaty's Law
Section 31: Cloak
Gateways: One Small Step
Constellations
The Lost Years:
The Lost Years
Traitor Winds
Mere Anarchy: Shadows of the Indignant
A Flag Full of Stars
Recovery
Second Five Year Mission Era:
Ex Machina
Star Trek (Marvel)
The Kobayashi Maru
Home is the Hunter
Enemy Unseen
Mere Anarchy: The Darkness Drops Again
The Covenant of the Crown
Timetrap
Rihannsu: The Bloodwing Voyages
Rihannsu: The Empty Chair
Shell Game
Death Count
Deep Domain
Academy Era:
The Pandora Principle
Enterprise-A Era:
In the Name of Honor
Probe
The Rift
Unspoken Truth
Mere Anarchy: The Blood-Dimmed Tide
Excelsior: Forged in Fire
The Lost Era:
The Last Roundup
The Captain's Daughter
Vulcan's Forge
The Lost Era: The Sundered
The Lost Era: Serpent's Among the Ruins
Vulcan's Heart
TNG Era:
The Lost Era: Well of Souls
The Lost Era: Catalyst of Sorrows
Vulcan’s Soul 1: Exodus
Vulcan’s Soul 2: Exiles
Vulcan’s Soul 3: Epiphany
I basically dismissed all the run of the mill five year mission stories, and only took the 2270's era stories where the uniforms on the cover and in the book matched what should have been used during that period. So those two requirements cut out several dozen stories.

I'll comment more if there are any questions. Enjoy!