Back-of-a-napkin simulation, one train every other minute out of each penn and grand central, 5k per train (long trains with people standing), about 24h. So not terrible, but would require both lots of planning, lots of resources (especially enough rolling stock to get people to where is safe and then return empty in time to not have gaps in the schedule), and great execution.
You could probably augment this by using the subway to get people out a bit and then having more places to change, depending a bit on where the bottlenecks are in the rail system. Also depends on how far they need to evacuate, are [some of] the endpoints of metro north good enough?
Highways might help if few enough use them, but the problem there is that capacity goes down significantly once overloaded. But in terms of a mass evacuation, it'd probably be best if the roads were kept reasonably clear for buses and evacuations for the elderly and sick that can't stand upright for an hour or two.