The movie was shot in Vancouver, British Columbia, Canada & New York City. However filming in New York only lasted one week. They couldn't afford to film there for longer. Only two shots were actually filmed there.
All the scenes with the ship were actually filmed inside the University of British Columbia's Ocean Research Center.
The toxic waste scene was filmed in an abandoned school's gymnasium
David Fisher, production designer, oversaw the construction of a one sided wooden cruise ship replica, which was placed against a big water tank.
The subway station scene was actually created as well. It was in downtown Vancouver's transit tunnel, and again David Fisher's crew set up several dozen feet of authentic looking subway track. They also had a back end of a subway car with an official New York transit logo on it. The tunnels they filmed in were originally made for carrying mail from the train station to the post office.
In the beginning of the movie, there is a brief shot of Camp Blood, that is actually a real camp for Boy Scouts in Vancouver.