Which pass you have planned to used is also a factor.
If you have JR East Pass (either one),
addtionally you can consider JR-Tobu through express from Shinjuku
If your itinerary calls for travel beyond Tokyo plus the above, then you need to post your entire itinerary to determine which pass pays off.
the fastest way is by shinkansen, but it takes 2hrs, costs more than 5000 per person for a non-reserved seat.
it takes 3 hrs by bus, costs half price of shinkansen, but with a reserved seat. It depends on how you weigh between time and money.
You don't have to use Shinkansen. Use one of the Tobu passes and it doesn't cost that much. See the link I posted in #5.