when are planning on coming first off, second thing, Madam Tussauds gets busy, as does the Planetarium. However visit Borough market during weekend, lots of interesting foods, plus some good pubs like the Market Porter right there if you want pub lunch, also gets busy. Greenwich is a good place for the Royal Observatory, it's a walk up the hill, but worth the view on a nice day. Definitely take a river boat if you can, as that offers some excellent views of all the interesting and not so interesting buildings, and if lucky you will get a good guide, one who actually knows his stuff.
Also Gabriels wharf along the south bank, and the National theatre, you can walk along way on the Thames path.
Covent Garden is ok, but is packed to the gunnels at weekends, but does offer some free entertainment, or where you put a quid in a hat for the entertainer. Do be wary of the hotspots as thieves lurk. Petticoat market by Liverpool street on Sunday only, most of it's tat, but worth a visit.
I could name a thousand places, most unknown to your average punter, have a good time