scappy, when you speak of getting into your desired "department," are you referring to a particular area of law? If so, which area of law do you like? With this info, maybe we can shed some additional insight into the DOJ vs. NYC Dept. of Law decision.
In any case, though, based on the information of the other posters, I would take the NYC position because it has a good probability of leading to a full-time position, unlike the DOJ position, and also because you like the NYC area. Also, remember that a bird in hand is better than two in the bush, much less one in the bush (which would be the case if you took the DOJ position).