USB 3.0 is as fast as eSATA and depending on your usb 3.0 device can be faster....but usually isnt. ;)
It really depends on your device as eSATA is bascially the same as internally connected hdd...and usb 3.0 basically is the same as well BUT there are a couple insanly fast USB 3 flash drives & raid drives that will destroy a single esata drive and tie a eSATA raid enclosure of the same size.
USB 3.0 is also a heck of a lot easier to use, but it costs more as esata can be used with a simple adapter off an internal mobo header whereas usb 3 needs a usb 3 controller (either on the mobo or via pcie daughter card). It really depends on YOUR needs, and YOUR setup WRT which is "best".
Personally I would go USB 3 (as that is what I have done). Its just easier than eSATA and works even on USB 2 systems that dont have an esata port.
IF I am reading your post correctly you are saying the ENCLOSURE is going to cost you close to 1 bill? That is insane! Get a USB 3.0 only one. They are cheaper and go for about 50.
When it comes to USB 3 enclosures you want one that uses the ASMedia chipset and NOT the one that uses the JMicron one. The ASMedia based enclosures all have the same speed...its just the enclosure fancy extras that differentiate them (same with all the JM...as they are ALL slow). The only major reviews I have read with eSATA have a distinct advantage over usb 3 all uses JM controller based devices for their test OR they were using outdated firmware. There really isnt a dif big enough to go A is faster than B ;)
With USB 3.0 you NEED to make sure the firmware and drivers are up to date as the mfg'ers page for the various usb 3 controller adapter cards (and mobos with it built in) are almost always out of date.
Get the latest drivers & firmware here:
SONY/NEC firmwares
IF you need a USB 3.0 controller...THEN go eSATA assuming you have eSATA. IF you dont have eSata or the adapters to make eSATA...spend a couple bucks for a x1 PCIe card OR a couple more for a faster x4 PCIe card (the x1s are slower than the x4 adapter cards even though they all use the same NEC controller).
Here is an example of a USB 3.0 enclosure that uses the ASMedia chipset:
NCIX.com - Buy Vantec Nexstar 3 SuperSpeed USB3.0 3.5IN SATA Hard Drive Enclosure Black - NST-380S3-BK In Canada.
IF you want more speed than what a HDD can provide you will need to go SSD route. A entry level 128GB SSD will smoke a HDD in speeds.
BUT remember its all well and fine having 200MB+ speeds BUT if the internal hdd's you are pushing and pulling data to/from are only good to 120mb....its a waste. ;)