I personally love the American Legacy "Underground Tours" that take place downtown and in Over-the-Rhine. They have a variety of tours that lead both locals and visitors through a historical journey of Cincinnati. I have personally done the "haunted" tour, but have heard great things about the original "underground" tour as well. They give you a chance to explore the origins of Cincinnati history and see the beautiful buildings and landmarks that add to Cincinnati's charm.
One of the most popular sightseeing tours I have heard of is the Segway tours of Downtown, Riverfront and Eden Park. I have never personally done a full tour but I have tested out a Segway from the group at the University of Cincinnati and it was a blast! Its defiantly not as nerdy as it looks. http://www.segwayofcincinnati.com/what-we-do/tours
The Duck Boats start out in Newport, near the Aquarium, then they cross the Ohio River into Cincinnati. They tour parts of Downtown and then take you back to Newport via the river. (newport.ridetheducks.com/boarding-info.aspx)
The Cincinnati Trolleys do charter tours for groups. (cincinnatitrolley.com/services/queencitytour.html)
There's also a self-guided tour of the city if you follow the Queen City Tour. signs. Look for a series of purple signs with QCT or Queen City Tour and follow them. (queencitytour.blogspot.com)