Navy Pier really is a tourist trap. There's not much to do unless you do go up the Ferris Wheel and there are far superior restaurants in the Windy City than Jimmy Buffet's Margaritaville.
BUT, if you must go, try scheduling an architecture boat tour that leaves from Navy Pier. I was glad I was able to kill two birds with one stone. The ferris wheel is pretty, isn't it? A great place to photograph.