My favorites (ones in bold are near public transit):
http://www.lulacafe.com/ (does a vegetarian tasting menu that is awesome)
http://rootstockbar.com/http://www.irazuchicago.com/http://urbanbellychicago.com/http://www.ruxbinchicago.com/site/Best wine list I've seen in a long time:
http://telegraphchicago.com/Not veggie friendly, but if you are into beer:
http://bangersandlacechicago.com/High end vegetarian spot, I have not eaten there, but have eaten at the chef's other restaurants, and would recommend it on that alone:
http://www.greenzebrachicago.com/awesome veggie only South Indian in the heart of Chicago's South Asian neighborhood:
http://www.mysoretogo.com/