A boat trip to Greenwich- there is the Cutty Sark and the maritime museum, the park is lovely with a good playground.
You can book free tickets to the Sky Garden which gives great views over London, but book in advance.
The V and A has a lovely courtyard with little paddling pool where you can sit and have lunch. Somerset House has water fountains which the kids can run around in while you sit and have a coffee- (take a towel) the Southbank has similar fountains. Somerset House currently has a Cute exhibition with lots of Hello Kitty themed items.
The Horniman museum in Forest Hill ( train from London Bridge) has a butterfly house, little aquarium and currently a small dinosaur exhibition, very child friendly with lovely gardens.
Young V and A is worth a visit- lots of activities for little ones.