Der_H and I have been planning to play BFG games set in the heresy era, with a hodgepodge of rules.This page
has amongst it a list for Inquisition fleets, including Black Ships. (As battleships, not cruisers, but it's all at your discretion when you're playing count-as and homebrew).
As for modelling, Black Ships are meant to be just that; sleek, dark and dangerous looking. So I don't think a lumbering battleship would work visually. (Although it may be fitting rules-wise). Maybe a battlebarge would portray a vessel that would voyage from system to system taking the Emperor's tithe. The landing bays and troop capacity would represent a ship capable of herding the dengerous minority into its dark holds, with the firepower and durability to keep them there if ever attacked.
On a smaller scale, a strke cruiser would fit this bill as well.
Then, your choice of escorts is up to you. (Excluding post-heresy designs naturally).
'The Voice' in Tales of Heresy
probably has descriptions of Black ships in it; certainly it should inspire you anyway!