This answer really depends on where in Tokyo you are going and at what time. I usually stay in the Aoyama area and am pretty comfortable navigating the trains so I take the Skyliner and transfer to the Ginza line at Ueno. This is not the fastest or the easiest way, espeicially if you have luggage, but it's a good compromise between easiest and cheapest. It does involve a bit of a walk and some stairs, so I wouldn't recommend it to a first timer with a lot of luggage unless they are arriving at a non-rush period (no earlier than 10:00 a.m. and no later than 2:30 p.m.) The Ginza line can also get extremely crowded (as can just about any train line in Tokyo) at any time of day so the bus is probably the best option if you have more than a carryon bag.