How can I make my 27" iMac and my 27" Thunderbolt display the same height?

I'd recommend buying this book:

http://www.amazon.com/Life-Times-Thunderbolt-Kid-Memoir/dp/0767919378/ref=sr_1_7?ie=UTF8&qid=1330596630&sr=8-7

It's exactly 1" thick, put it under the monitor.

If you want something more elegant than a book under the iMac, you can can add vesa mounts to your iMac and Thunderbolt display and then attach it to a desk or wall mounted adjustable monitor arm. There are many to choose from but here is one pictured below to give you an example. So you could technically mount both or just one to a VESA stand. Note that most monitor stands allow you to infinitely adjust the height, angle, rotation, with in pre-determined ranges.

Just be aware of the maximum weight capacity of the VESA monitor mount you choose. The 27" iMac weighs 11.2kg or ~ 24.7 LBS and the 27" Thunderbolt display weighs ~ 10kg or ~ 22.1 LBS without their included stands.

Looks a product was created for this task. Checkout the HiRise by Twelve South as reviewed by MacWorld. Boom iMac and Display = Level.

Mac accessory maker Twelve South has introduced the HiRise for iMac, a stand that lets users elevate their desktop Mac monitors to a better viewing level.

The $80 device is designed to support all generations of Mac that have an L-shaped stand, including the largest 27-inch displays on the latest generation of iMacs. The stand itself looks a little bit like an older, metal-shelled hard drive—a reminder of the days when drives and displays were separate components of the same computer.