If you are not carrying too much luggage then you can take the Airtrain to the subway's A Train into Manhattan. It is $7. A great deal if you have the time and aren't lugging around too much. If you want the ease of taking a taxi it is a flat fee of $45 plus toll & tip. If you decide to take the Midtown Tunnel (most direct) it is an additional $5 toll (I believe). Otherwise the driver would take one of the free bridges.
If you take the A train into Manhattan you can buy a Metrocard at the station (a good thing to have in the city anyways) and put at least $7 on it to get into the city. The same card can be used for the air train and the subway. When you get to the Times Square station get off and wait for one of the local trains to take you to the 50th street station. It is on the same platform and is the E or C train. There's no elevator or escalator at that station therefore I advise this scenario if you are comfortable lifting whatever luggage you bring. The Novotel Hotel is very close to this station.
Have fun!
Transport