There is a relatively cheap train ride from Newark into NY's Penn Station. I think it is a NJ Transit commuter train. I've never done it but I'm sure it will be well marked. Unless you don't have any luggage, you'll probably want to take a taxi to your hotel.

As to hotels, your best bet is to use Hotwire in conjuction with betterbidding.com You will probably be able to identify the exact hotel that Hotwire is offering you. (Hotwire is an "opaque" hotel site but unlike Priceline you don't have to bid. Priceline is probably 10% cheaper, but you have to pay your money upfront. Hotwire you only pay if you like the price/offering.)