Craft beer cellar by the mall has a decent variety of local beer. There are also a couple grocery stores with good local beer selections (Rosaurs or town and country on 11th ave). You won't find much for local wines just FYI.
Here are some of my personal favorites:
1. Madison River - hop juice double IPA or copper johns
2. Bozone - Amber or IPA
3. Kettle house - coldsmoke (from Missoula)