The largest 3 of the "craft" breweries are Schell, Summit, and Third Street. Schell makes a decent Alt and their Snowstorm beers are usually pretty interesting, otherwise more of a mainstream brand. Summit is also pretty large and makes a good IPA called Saga. Their Maibock is good, and the Extra Pale Ale (semi Macro) has been a favorite for decades here. Third Street has a couple of good ones, but stay away from their Bitter Neighbor Black IPA. Its like bottled up ashes IMO. Their Lost Trout Brown is pretty good.
As far as the smaller breweries go, there are some good ones. Surly of course is well known. The Furious is their flagship and puts an interesting spin on the IPA with their Golden Promise malt and Simcoe hops. I like their coffee Bender and their wet hopped IPA is awesome too when in season. Darkness is another limited release beer, but difficult to find. Fulton makes a decent IPA and a couple of other respectable brews. Brau Brothers, Lift Bridge, Town Hall, Big Wood, Leech Lake, and Lake Superior are some other small ones that I've tried.