Tokyo station or Shinjuku area to stay

Hi ,we are a group of 5,please help me choose the area to stay.
-We will reach Narita 16.00 then take Nex or limousine bus and stay 1 night in Tokyo and left luggages there.
-2nd day go to kawaguchiko by fujikyu bus from Shinjuku stay there 1 night.
-3rd day back by bus and stay 1 night in Tokyo .
-4th day take shinkansen nozomi to kyoto in the morning around 9.00 or 9.30..
then stay 2 nights in kyoto and 1 night in osaka before left Japan from KIX.

I hesitate between stay that 2 nights before and after Kawaguchikoat hyatt regency shinjuku which i will get the very good rate . but on the 4th day Ito catch the shinkansen I have to take taxi to tokyo station , how will the traffic be at around9.00 am and how long will it take?

or should I stay near Tokyo station such as Ryumeikan or Metropolitan marunouchi hotel with the 10000 jpy higher per night per room.

thanks.

Well, you could spend most of your nights at Shinjuku, then just that one last night at Tokyo station.

Or don't bother with a taxi, and just take the train to Tokyo station from Shinjuku. If you're traveling around 9am, the morning rush should pretty much be over by then.

to catch the Shinkansen I have to take taxi to Tokyo Station

No, you do not have to do so.
In Tokyo, Tokaido Shinkansen of JR-Central is available in Tokyo and Shinagawa Stations.
(Maybe you read something about a Shinkansen line of JR-East, which is available in Tokyo Station but not in Shinagawa Station, and thought as if it were your Shinkansen line.)

Hotel Metropolitan Marunouchi and Hotel Ryumeikan Tokyo are near Nihombashi Gate for Tokaido Shinkansen tracks of Tokyo Station.
Shinjuku Highway Bus Terminal are away from these two hotels.

From Hotel Metropolitan Marunouchi you can walk also to recently-restored Marunouchi Entrance of Tokyo Station.
From Hotel Ryumeikan Tokyo you can walk also to Nihombashi Station of Tokyo Metro, from which you can use Ginza Line to Ginza, Asakusa or Ueno.

Hyatt Regency Tokyo is near Shinjuku Highway Bus Terminal, where you will take a bus for Kawaguchiko.
Tochomae Station on Toei subway Oedo Line is close to this hotel.
Near this hotel are Tokyo Metropolitan Government Buildings Nos. 1 and 2.
TMG Government Building No. 1 has observatories at about 200 meters from the ground, which are open to the public free of charges.

A route from Hyatt Regency Tokyo to Kyoto Station:
Hyatt Regency Tokyo
--Walking--
Entrance A7: Tochomae Station (E-28): Track 1
| [Toei subway Oedo Line: Train, about 5 min., 180 yen]
Track 1: (E-26) Yoyogi Station: Exit A3
--Transfer--
North Gate: Yoyogi Station: Track 2
http://www.jreast.co.jp/e/stations/e1654.html
| [JR Yamanote Line�fs inner loop: Train, about 20 min.]
Track 1: Shinagawa Station: Shinkansen South Transfer Gate
http://english.jr-central.co.jp/info/station/_img/shinagawa_L.jpg
http://www.jreast.co.jp/e/stations/e1654.html
| [JR Tokaido Shinkansen]
Kyoto Station.