No way to Buck House / Trafalgar Square. Awfully crowded touristy and totally boring for a 6 year old. Yes to the Thames Clipper. I'm a Londoner and this is what I'd do with your timeframe.
From Kings X get the tube to London Bridge (Northern Line 10 mins), then exit at Tooley Street and walk to the river by More London / London Assembly to the clipper stop at London Bridge City. This will be a 10 minute walk from where you'll see a spectacular view of Tower Bridge, HMS Belfast, the river and the city across the water.
Take the clipper a few stops down to the London Eye - great fun. En route you'll pass many famous buildings including Shakespeare's Globe, Tate Modern, Harry Potter bridge etc, and if you sit outside at the back of the boat your 6 year old will love it!
At the London Eye you could obviously go on the eye if you fancy it, or alternatively just walk along the southbank which has plenty to see including street performers, stalls and the skate park. Here there are a number of good restaurants suitable for your 6yo underneath the southbank centre / Royal Festival Hall, all overlong the river. Eg Giraffe , Wagamama's etc etc, or the restaurants at the BFI Southbank.
From the southbank you can walk across either of the bridges and turn left (west) to go to Westminster to see the Houses of Parliament, and/or to St James Park to see the pelicans, or alternatively turn right (east) to walk to the Strand, Covent Garden etc, where in the piazza you'll see street performers, magicians etc. A straightforward tube back to Kings X.
Hope your 6yo really enjoys the day!