The Reef-- Awesome selection of corals (the best that I've found in central IN). Pretty good selection of fish too. Located on Keystone Av.
Uncle Bills-- There are locations on the west, east, and south sides of Indy. Unfortunately, you'll be on the westside and that location is not the best of the three. If you have time check out the one on the southside. East St in Greenwood.
The Abyss-- Great place too, verts and inverts. 62nd St in Indy... only open from 4-7 during the week!
When you get here check out the yellow pages and call these places for specific driving directions. Have fun! If you have kids, be sure to check out the Children's Museum.