If you are going through Omaha you have to make time to go to Nebraska Brewing Company. Try the Hop God, Melange a Trois, Black Betty, or any of their regular beers, you wont' be dissapointed.
Krug Park is hands down the best beer bar in Omaha, Crescent Moon and the beer store next door are very good. Blatt Beer is a great new bar that just opened up this summer.
In IA, there is a new brewery in Okoboji. I haven't been there or had the beers but that would seem like a no brainer.