There aren't that many...
I'll recommend Rogue Saucer and Double Helix: Quarantine, both by John Vornholt, both nominally under the TNG imprint. The first deals with an attempted Maquis hijacking involving the E-D crew, the second follows Chakotay's cell as they investigate a plague outbreak on a multispecies world (also tells the story of how Tom Riker joined). Apart from that, Book 2 of KRAD's The Brave and the Bold has Chakotay and Cal Hudson working together.
Fictitiously yours, Trent Roman