Not all vaccines are created equal. We know many rescues who get them online. We just get them from Del's feed stores. If they are not kept at a proper temperature, they are worthless. Del's is the only feed store in our area who does not have a history of dogs getting parvo after using their vaccinations.
As for your litter, the vet should have a "litter" price to check them all out and give them the first vaccine at 8 weeks. It should be NO WHERE near $1000! You should call around for different vets.
You can also google low cost spay/neuter in your area. I've done it for many here when I know where they live at.
That's a lot of money and you do not have to spend near that much! No more than $10 MAX for a DHPP shot. That's $60ish for the puppies and a flat litter checkup fee at a vet.
We use several vets with one primary vet. They are not all created equal and some of the fee difference are astounding (dental: $400 at one $125 at another for the same dog!).