Can my employer dictate what financial institution I have to deposit my HSA contribution into or am I able to deposit it in the place of my choice?

If your HSA contribution is part of your own separate contribution and is not tied to a group contribution account, you can make your deposit into any approved bank account with such HSA designation as you desire. From what you have written, most individual as opposed to group HSA contributions are placed in bank accounts that the individual contributor desires where his or her employer has no choice in the matter.

Your employer may be able to require it. However,  see if there is an option to simply have it forwarded to your institution. This is less of a choice if there is a benefit tied to having it at a particular institution. Check with your provider.