Daxter is a very very very better than TLF. It features Daxter in the 2 year gap when Jak was captured but I'm guessing you already know that. The story was better. It showed Daxter could step up to main character in a game. The gameplay is really fun as well.
My personal favorite, would have to be Jak & Daxter: The Precursor Legacy. I liked the standard platformer feel, and the simplicity of the combat. Granted, I love Jak II and 3 as much as the next person. Definitely my favorite games to Platinum .
In my opinion it'd have to be Jak 3, simply becuase it combined the more platformy feel of the original Jak and Daxter yet still carried over the ragged-feel of Jak 2, but still mad respect Precursor Legacy.
In my opinion, Jak 1 was the best because it was the most polished. Whenever a new gameplay mechanic was added in the sequels, it usually needed improvement.
However, Jak II & 3 deserve credit for showing that Naughty Dog was becoming better at storytelling.
To me, Jak 3 was a masterpiece and is still one of my favorite games of all time. My list of how I rank the series:
1) Jak 3
2) Jak 2
3) Jak and Daxter: The Precursor Legacy
4) Jak and Daxter: The Lost Frontier (I actually really liked it)
6) Jak X