"Algonquian" is not a language; it's a family of dozens of langauges spread over eastern and central North America. Potowatomi and Ojibwe are two Algonquian lanugages near Milwaukee, so those are likely candidates. Because the Algonquian languages are all related and share similar roots, it's probably impossible to tell which language the name came from unless there are historical records that state the source.
Algonquin, however, is an individual language (or dialect), the one the family is named after. However, it was spoken in Quebec, far from Milwaukee, so it's not a likely candidate.
Perhaps from Potawatomi minwaking, Ojibwe ominowakiing (“gathering place (by the water)”), or an Algonquin word meaning for “the good land”.