We stayed in Jersey City two weeks ago for our visit to New York. We stayed at the Marriott Courtyard, which also had a PATH stop right next to the Hotel. It is not waterfront like the Hyatt (which was the other hotel we considered), but the Courtyard had free wireless, queen beds, and cheaper valet. The Hyatt charged for wireless, had double beds, and valet was twice the price. And, the waterfront was just a short stroll fro The Courtyard, only one or two short blocks. I'm sure the Hyatt is a much nicer hotel, and part of me was bummed for not staying there, but The Courtyard was fine and really did make more sense for us. There was a nearby Target which I could see out of our window.
BTW, my boys would be so jealous of a Soho apt! They are 18 and 19 and loved the whole city, but the Soho area was by far their favorite!
Good luck!