One of the coolest way to enjoy Tokyo is cruising.
The routes looks little complicated even for Japanese, so simply the best route I recommend for family is the one depart from Asakusa goes to Odaiba. (about an hour)
If you could make reservation, definitely choose those cool ships – HIMIKO, or HOTALUNA, or EMERALDAS. (run by Tokyo Cruise company)
Those ship are designed by Reiji Matsumoto, famous Japanese manga artist.
The design looks like spaceship, makes fun cruise much more exciting!
Overall all boat crew are friendly, will help you to carry baby stroller.
I guarantee you and your kids would love Tokyo bay cruise^^