What kind of birds were infected in the NYC outbreak? Were they a migratory species and would their route have taken them thru Cuba? And where else on the flyway might they have nested and spread the infection?
As I'm writing, I'm thinking one of the infected birds in Baltimore was a crow...
Many different species of birds can be infected with West Nile virus. According to a CDC study of 430 birds in the New York City area, conducted in September, 1999, birds of the following species were found to be infected with WNV: Canada goose, domestic goose, mallard/domestic duck, domestic chicken, turkey, mourning dove, rock dove, brown-headed cowbird, and house sparrow. I don't know why crows weren't found in this study, but infected crows have been very common as well. I should add that these species are not particularly closely related.
I don't know about the migratory patterns of these birds, but it would appear that most, if not all, bird species can be infected by West Nile virus (as can many mammals).
This argues against the idea that migratory birds were infected in Cuba and then flew to New York City. If that had happened, we would have seen evidence of West Nile virus at some intermediate locations, earlier than the New York City outbreak or at least in the same time frame. But it's clear that the WNV outbreak first emerged in Queens and spread out from there.
By now it's spread to much of the eastern half of the U.S. It's possible that there were additional introductions in places other than NYC later than the NYC outbreak, but it's perhaps more likely that it just spread out from NYC. Either way, New York City is where it started.