For brewery tours there are Lakefront Brewery, Milwaukee Brewing Company, Sprecher Brewery, Miller (eh). All the tours are good, and you get bunches of beer with the tours, especially Milwaukee Brewing Co. Lakefront is probably the best known and is the best in my opinion. If you have kids, they'll love Sprecher because they have all you can drink gourmet soda.
For brewpubs there are Milwaukee Ale House, Water St. Brewery, St. Francis Brewery, Rock Bottom, Horny Goat Hideaway (dumb name, and ok beer, but awesome patio on the river), Stonefly Brewpub, Delafield Brew House & Sweet Mullets (both are West of MKE a bit). The Ale House and Rock Bottom are right on the River and a good place to hang with good weather.
There are great beer bars too. Burnhearts is my favorite, with more of a corner bar feel with killer beer & craft cocktails and shuffleboard. Sugar Maple specialized in WI and regional brews (60 taps). Cafe Centraal is a great Belgian beer bar and is next to Sugar Maple. Benno's is in West Allis and is a bit of a hole in the wall, but great beer selection. Roman's is a Milwaukee beer bar staple and comes complete with the owner's attitude and is a bit pricey in my opinion. Comet, Lulu & Honeypie are great for locally sourced home cooked food with great beers.
www.onmilwaukee.com is a good source to look at.
I hope this helps.
