Vine and Hop is a nice store in Madison. It is on Monroe street near Camp Randall Stadium. Friendly and helpful staff, but I have only been there once. Nice selection of grains and hops. Equipment selection is average. They crush grains for free, but that is common.
Brew and Grow is another place in Madison, but it should be called GROW and brew. The brewing stuff is confined to two small aisles in the front of the store, half of which is Brewers Best extract kits. The other 90,000 sq ft is dedicated to indoor reefer gardening supplies. The staff there doesn't know much about brewing, but they really like Phish.
There is a Zymurgy Outfitters in Oregon, WI, which is closer to Janesville. Never been there.