Thunderbolt 3 and USB3-C are both communication protocols that use a physically similar connector.
USB3-C doesn't exist. There is Thunderbolt and there is USB. There is also USB-C but this is only a connector and cable which can be used to carry either Thunderbolt or USB. Currently all USB-C docks are in fact merely USB docks so they don't use Thunderbolt 3.
The difference between USB and Thunderbolt can be quite big. The biggest difference is usage. Thunderbolt is also a more robust protocol meant for high speed data transfers (it has a higher bandwidth, lower latency and some other nifty stuff) whereas USB has been used for simple peripherals (keyboard, mouse, printers, etc.) and has been beefed up over the years (it now goes up to 10Gbps but it doesn't have the low latency Thunderbolt has). Because of this USB is quite simple and cheap whereas Thunderbolt is complex and expensive. You'd generally use USB for simple devices that any consumer would use and use Thunderbolt for more high end devices that professionals and demanding consumers would use. If you'd need a comparison: it's a simple 2,5" disk vs a 5-disk (or even more) RAID array.
So long story short: you'd get a Thunderbolt 3 dock when you need those higher speeds and/or when you want something robust. That's usually the case when you have something like a RAID cabinet, 4k 60Hz display (or even 5k), high end A/V devices, etc. If you don't have any of those you'd simply get the USB dock because it will work fine at a lower cost.
One thing to add: currently there are more USB versions than Thunderbolt 3 versions available so that would be one more reason to buy the USB version. Or a reason to wait a little
Thunderbolt 3 is a superset solution which includes USB 3.1 (10Gbps)...
USB 3.1 consists of 2 different kinds: Gen 1 (aka USB 3.0 which does only 5Gbps; this is used in the current and previous MacBook) and Gen 2 (used in TB3 and thus in the new MBP). Manufacturers really need to mention which gen their USB 3.1 implementation is, else there is even more confusion.