This article is from the NYPD Blue FAQ, by Dave Chapman, Alan Sepinwall and Jeff Knapp with numerous contributions by others.
No one knows for sure, but it's not hard to extrapolate that
she wasn't happy with the mess that was made of her character
in the third season. Rumor has it that she was difficult to
work with (and therefore may not have left of her own accord),
but who knows if this is true. Since leaving the show, she's
popped up as a guest star on a few shows (including "The X-
Files") and had a very small recurring role as a NY District
Attorney on Dick Wolf's "Feds," which is not likely to be
renewed by CBS.
Lesniak's departure was never explained. One can assume that
she transferred out of the precinct to avoid the discomfort of
working with James.