I can assure you that no matter what shoes you have on, there will be no doubt about your being American tourists. Loud voices (particularly in restaurants), sport style sun glasses, baseball hats, t shirts with various US sports team or school logos, over tipping, men wearing shorts, khakis, golf shirts; put it all together and it screams US tourist.
However, no one will really care and you want to be sure your feet are comfortable.
I´m not a big fan of the HOHO buses, at least not for Paris. They are very expensive and not a particularly efficient way to travel the city. However, the river cruises can give you a great overview as many of the most important sites are located along the river. I prefer Vedette du Pont Neuf and you can pickup reduced price tickets on their
website.
The Bateaux Mouches depart from near the Eiffel Tower. Their boats are bigger but their larger size allows people to thoughtlessly stand in front of you, blocking your view, a situation which I find most annoying.