I think you'll find that two RT ferry fares plus paying for parking will probably cost at least as much as a garage - and you can't miss the garage (as long as it;s open 24 hours) and then have to find car service and pay $60 or $70 to get to your car in Jersey.

If you can find a hotel in Manhattan for no more than $40 more than in NJ, then the price would be a wash. Try pricing the Aloft hotel in Harlem. Or the Yotel in Manhattan. You'll pay about $40 round trip for the ferry to NJ. For myself I'd try to find a Manhattan hotel and just pay a bit more if you can afford it. You'll be much happier if you aren't trying to get back to NJ late at night. Right now with transit not at 100%, it's challenging.

The best option is the Hyatt Regency in Jersey City, which is next to a PATH station and a ferry, but its booked for that night. But there might be a cancellation. OR try Priceline.