Sorry if I confused you! You may be able to re-check after customs, things are always changing and with the new security measures in place, who knows anymore!
I just flew domestically this week and the security was different at both airports. I would wait and call before you fly. They may have us re-packing in front of TSA by then!
I'm going to be at Newark, Terminal B on Monday. I'll ask, but I would call again closer to your travel date.
The runways at Newark are parallel to the NYC skyline. So yes, you can see NYC, but depends on the side of the plane you are on.