[[ I dont really think you can boot off a USB drive. Maybe USB3 is different from USB2 but I thought you couldnt use a USB drive to boot from. However I may be wrong. ]]
The poster who wrote the above -is- wrong.
I've been booting my 2007 iMac from a USB2 dock for years.
For the past year, I boot and run my late-2012 Mac Mini from a USB3 dock.
As stated above, the enclosure or dock that one uses "makes the difference".
To the OP:
Yes, you can boot and run the iMac just fine from either a thunderbolt or USB3 enclosure. Again, if you use USB3, you need to investigate and get the RIGHT enclosure or dock.
Be aware that you will pay a premium to use thunderbolt, and most drive enclosures are not going to provide an extra "pass-thru" thunderbolt port, so if you connect a thunderbolt external drive you probably won't be able to use the Tbolt port to connect a second display.
USB3 is much cheaper, will run just as fast.
For my own setup, I use a plugable.com "lay-flat" USB3 docking station. Not elegant, but it sits out-of-the-way on my desk behind the phone.
For an iMac, this might work:
http://www.amazon.com/dp/B003VKTJGW...UTF8&colid=R75PP4I2A0BE&coliid=I3DOKZ31SP7539
(might be available in silver as well, to match the iMac)
I've heard of guys attaching these to the back of the iMac stand with velcro tape.
IMPORTANT!
When you shop for an enclosure, you want one with an "ASMedia" chipset (1053e preferred), and be sure that it states that the enclosure supports "UASP". This is "USB Attached SCSI Protocol" which is based on the old SCSI standard and relieves the computer's CPU from dealing with USB transfers. Thus, much higher speeds with negligible CPU loading.
Also, Weaselboy is correct about not being able to enable TRIM via USB.
Also, you probably won't be able to run a firmware updater for the drive, if one is released.
I've found that recent versions of SMART Utility seem to be able to communicate with and report well enough.
If you can "live with the two limitations" mentioned above, USB3 is a "good enough" choice. I have no problems with it.