Greenwich market on a Sunday is meant to be quite good, never made it myself.
Shoreditch/Brick Lane area has some good warehouses, and the odd fly-by-night shop (I don't mean that they're dodgy, they just come and go quite rapidly)
Camden Passage in Islington, although I hear it's about to get redeveloped so I've no idea what will happen there.
Worth looking at yell.com for individual shops and charity shops too.
I hope you have a lovely time here!!