Captain's Table: Fire Ship is outstanding; in my opinion, the definitive Janeway story. And I like Infinity's Prism: Places Of Exile a lot, but a lot of Janeway fans (including, actually, Kirsten Beyer) aren't fans of Janeway's portrayal there, so that recommendation is a little more hedged.
In general, numerically or quality-wise, it's hard to argue against the fact that Voyager's gotten the short end of the stick when it comes to novels. It's hard to think of very many good Voyager novels period, much less Janeway ones. Voyager's prior relaunch didn't hold a candle to really any of the other ongoing serialized narratives, Voyager's numbered books are almost universally lame, Voyager's entries in all of Ordover's crossover series (with the Captain's Table exception) tended to be the worst of the bunch, and even String Theory began brilliantly but ended on a kind of sour note.
In fact, aside from Beyer's books, Fire Ship, Infinity's Prism, and the first String Theory entry, I can't think of any Voyager books I've liked very much. I haven't read Mosaic or Pathways, though.