Friendly Airport Limousine Bus 2000-3000yen (Depending on distance)
(ask for a free 1-day subway pass when purchasing)
Pros: comfortable, no transfers, door to door to many hotels throughout the city, free wifi on the bus, luggage stored by the driver, easy to sleep through the trip, hotels can arrange a taxi for onward travel, the no-hassle solution
Cons: less to see along the way, a bit slower than the train, no drink services or toilets
Keisei Skyliner Express Train 2400 yen (to UENO)
Pros: quick at getting you into the East side of the city (Ueno), cheap, comfortable.
Cons: if staying on the West side of the city (Shinjuku, Shibuya, Ebisu etc.) requires a change of trains and about a 30 min ride on busy commuter trains
JR Narita Express 1500-3000 yen (includes transfer to any JR station in Tokyo Area)
Pros: Fastest way to the West side of the city, drinks and snacks sold onboard. Return tickets with Suica card are a good deal. If activating a JR pass the best bet.
Cons: if not staying at a main station you will have to get on a crowded commuter train with your luggage to get to your destination
Keisei Bus 900 yen
Pros: the cheapest
Cons: Not very good website, bus stop is a bit difficult to find, have to go to Tokyo station in order to catch the bus