Getting about in Tokyo, and Japan in general, is pretty easy. Although the crowds can be daunting, there are usually sections reserved in trains and on buses for pregnant women and people travelling with children. Look for 優先席 (yuusen seki)
TRAVEL WITH STROLLER
A large number of stations have elevators but some do not. To check station accessibility with a stroller:
If the station does not have an elevator, there is an inter phone at the top and bottom of all stair ways. You can use this to ask for station staff to help you with your stroller or pram.
Most buses in and around Tokyo are non step buses and you can take your stroller on these buses easily. The entrance can be rather narrow though so, depending on your stroller, you may be asked to enter from the side doors on the bus.
Most of the large department stores and shopping centres have nursing rooms. Many of these will also have hot water dispensers for making up formula.
Look for 授乳室 (junyuu shitsu) signs. Often they will be marked with a baby bottle symbol.
For iphone users - download Milpas for your nearest nursing room/changing facilities
For Android users - マママップ will give you the same service
To find out which airplane seats are children and baby friendly, check the seating arrangements on this website http://www.seatguru.com