I am planning to visit NYC in May. Is there an expensive way to get to JFK for a 7:00am flight? I will be staying in Times Square area. The first bus leaves from the Port Authority to JFK is at 6:00am. It wouldn't work. Do A or E trains run in a relatively frequent schedule during early Monday morning?

Let me suggest, as a alternative, going ten blocks south to Penn Station, and taking the LIRR train to Jamaica, where you can also take Airtrain to JFK. Its quicker and more comfortable, and oly slightly more expensive ($4.75 vs $2 for the subway). There are trains at 5:11 and 5:26 which run nonstop and get you to Jamaica in 20 min. Taking the subway at an early hour will be much longer, and because of the recent fire, you'll wait longer for a train.