The other option is to stay outside of New York City.
Please check the link at http://mta.info/mnr/html/mnrmap.htm for Metro-North Railroad.
Any place beyond North White Plains on Blue(Harlem) Line or something similar on Green(Hudson) Line will be very safe and quite.
You can find an inn(or B&B) close to the train station and take the train to Grand Central Terminal every day like most white collars do.
In this case, you can drive your car to the town and leave it either at the inn or at the station(paid parking) depends on how far between the station and the inn you stay.
BTW, Manhattan is the safest area in New York City.
As long as you stay in the lower/midtown during the day and go back to your small villa not too late, you will be as safe as here.