I should probably be ashamed that my top thing to do in any city is find the nerd spots. Here are two of my favourite from my last trip to the US.
B&H Photo in NY is probably one of the coolest stores in NY. They have this amazing conveyor system that makes them feel more like an Airport than a store.
Autodesk Gallery in San Francisco is another hidden gem. An amazing space that celebrates the massive variety of things that Autodesk software has been used to design and build.