The hotel with the park, ride and cruise package
@msmama was referring to is the Hilton Garden Inn in Ridgefield Park, NJ. You have to book that specific package which you can find under Special Offers on their website. We used them in 2016, and have them booked again for next fall. It is a really nice hotel in a safe area (or at least it seemed to be), and having a car service take you to and from the pier makes it a winner for us. We are on a 10 night cruise next fall, so at $40 per day to park at the pier, just parking alone would cost more than we are paying for the entire hotel package.
We had no problems sailing out of NYC - actually we loved it. The views are incredible and we love that we can drive vs. having to fly - big cost saver. I remember long lines in security and check in, but it moved pretty quickly. There was a slight delay in getting on the ship, though I never really knew why. We have sailed out of lots of different ports, and they all have their own little quirks. At the end of the day no matter where you sail from you are going to drop your bags with the porters, go through security, get in line to check in then have a seat and wait for your number to be called if it's not already open boarding when you arrive. No big deal.
Have fun!