Since you'll be relying on this for storage, because the internal storage is relatively small, thunderbolt. Without a question. You've already shown you can pay a premium price. Thunderbolt for you, without a doubt.
it makes not one bit of difference. The speed of the USB3 vs Thunderbolt interface is getting into splitting hairs. Unless you are going with a multi hard drive RAID0 case then you will be limited by the drive speed. Even a single SSD can't exceed to throughput enough to clearly justify one over the other.
Just buy what is available at a price you are willing to pay.
If the external drive is a single spinning HD, you will not see the speed benefit of TB. The drive itself is too slow. You are just as well off to get a cheaper USB 3 enclosure.
If the external drive is an SSD, then you have two choices. The first is to put the SSD in a USB3 enclosure that does the UASP protocol. The second choice is a TB enclosure. The performance would be about the same with the USB3-UASP enclosure being cheaper.
BTW. don't forget a separate external drive for backups!
Check out Samsung's T1 or the new T3 SSD external drives. The T3 comes in a 2 TB capacity plus smaller sizes, and the T1 is available in a 1 TB size as well as the smaller capacities. This is a very fast, physically small bus-driven USB 3.0 connection external drive that works well as a supplemental drive when one has a computer with limited SSD capacity. I bought a retina MacBook Pro (512 GB SSD) in December and shortly after setting it up also purchased a 1 TB Samsung T1 to use as a supplemental drive. I also have various other external drives that are used for backup purposes. The T1 or T3 are not inexpensive, but I think that the SSD speed and the incredibly small size, great for travel, makes it worthwhile.
If you're after more capacity than this, since you're using a desktop machine and portability might not be all that important to you, the Seagate Backup Plus drive comes in various capacities, I think up to 4 TB, perhaps more, and it again plugs into a USB 3.0 port.