GA
Yes, I've known people who have stayed there in the past for concerts at MSG and they have some hair raising stories.
If anyone is looking at hotels down near the WTC, I wouldn't rule them out.
The 1/2/3 and A/C/E lines go straight down to that area from Penn Station and it's totally safe at night. Plus, downtown hotels on the weekend might be a bit cheaper than something near Times Square, since they are predominately business hotels.
But I don't know too much about finding good hotels in the City, as when my friends come to NYC they just stay with me. I just wanted to mention the Hotel Pennsylvania, as I've heard it often comes up on Hotwire. Sounds lucky that you ruled it out!