I don't know Weehawken too well. It is quieter I believe, not sure about safer. It's not as walkable as Jersey City or Hoboken. And also not as convenient for commute to lower manhattan. I think you have to either take the lightrail to hoboken to catch the PATH or you can take the ferry to midtown and the subway/bus.

I used to work in the LES before my office moved to Brooklyn. If you want to make your wife's commute less hellish, try to stay near the PATH. Maybe consider Harrison. There's loads of new buildings there due to building up the area near the PATH and the soccer stadium, a lot of new restaurants...