For midtown, I've come to favor the bus over the train from EWR. You get on the bus immediately outside of an arrivals terminal. It is express, so only 3 stops in midtown: Port Authority bus terminal, Bryant Park/NYPL, and near Grand Central Terminal. The airtrain seems maddeningly slow then you have to wait for the NJ Transit train and it isn't so convenient with luggage and you won't get a seat if busy.