: I will be staying in the Tokyo Disneyland area, and the nearest train station is Maihama which is on a JR East Keiyo line.
: I suppose that's my start point for visiting the rest of Tokyo. - Trains from / to Narita Airport do not run via Maihama area. If you arrive in Japan at Narita Airport, then it sounds not nice to first visit Tokyo Disney Resort [TDR] then head for Tokyo. (TDR is not located in Tokyo Prefecture, to be precise.)
- Reading your post, I see no reason to recommend your lodging in Maihama area for other nights than the nights before you visit TDR.
- If you have enough time before this journey, then I suppose it's worth trying a hotel / ryokan in other areas, though maybe that does not perfectly meat your requirements.
: I will be having 2day free tokyo metro pass, can these be used on JR East line?
: there a stored value card that can be used on both tokyo metro lines and JR East?
- A Tokyo Metro Pass is valid for 9 subway lines of Tokyo Metro, which is one of the two operators of subway lines in and around Tokyo. Another operator is Tokyo's Bureau of Transportation, whose 4 subway lines are usually crowned with "Toei": Toei Oedo Line, Toei Asakusa Line, Toei Shinjuku Line, Toei Mita Line. No Tokyo Metro Pass can be used on these 4 lines.
- If you have already decided in details the spots to visit in Tokyo, then I suppose it's better to seek the routes comfortable for the spots than to pursue a value ticket / pass for such short-distance trips.
: For my one week stay, I assume I'll have to take the train from Maihama to Tokyo station and transfer to various subway lines to get to places like Shinjuku and Sensoji temple. Right?
- Only one subway line has Tokyo Station: Marunouchi Line of Tokyo Metro. The platform of this line is relatively near that of Keiyo Line of JR-East, but the transfer still requires a bit long walk.
- You can make a gate-to-gate transfer at Shin-kiba Sta. to Yurakucho Line of Tokyo Metro / Rinkai Line of TWR.
- For Sensoji Temple, you can take this route:
Maihama --[JR-East: Keiyo Line]-- Hatchobori --[gates]-- Hatchobori --[Tokyo Metro: Hibiya Line]-- Ueno --[Tokyo Metro: Ginza Line]-- Asakusa.
- Your route for Shinjuku area depends on your destination.
- As is mentioned in other posts, you'd better avoid as possible a transfer at Tokyo Sta. between Keiyo Line and a line on the ground. If the two children are little but not so light to be carried, then the transfer can be a nightmare for them after getting comfortably tired in Tokyo Disneyland.
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