Well, I won't claim these to be the "best" necessarily, but they are some of my favorites:
The Wounded Sky
; My Enemy, My Ally
; The Romulan Way
- Diane Duane - Three of the better TOS-era novels. The Wounded Sky especially captures a sense of wonder that few other Trek novels seem to. Diane Duanee captures the voices and personalities of the TOs characters better than any other writer has.
The Galactic Whirlpool
- David Gerrold - from a story he orginally pitched to the TOS production staff. A TOs story from someone who actually wrote TOS we saw on-screen. This book has a lot of really fun little details in it.
How Much For Just The Planet?
- John Ford - TOS as a musical comedy. Really.
- Barbara Hambly - TOS meets Here Come The Brides
- Judith and Garfield Reeves-Stevens - Would have made a really good finale to TOS. Epic story.
The Entropy Effect
- Vonda McIntyre - Best of the early Pocket publishing era. A couple shocking plot twists. If you don't read any of the other books I've listed here, be sure to read this one.