How do I choose between freelancer and agency?

You are buying different things. With a freelancer you buy one person's attention and talk to whoever writes the code, so decisions are fast and context is never lost in a handoff. With an agency you buy a process and a bench — project management, cover when someone is ill, several disciplines at once — and accept a layer between you and the work.

The risk each carries is worth naming. A freelancer is a single point of failure: if they become unavailable, the project stops. An agency's risk is that the person who sold you the work isn't the person doing it, and quality varies with who is free that month. Either way the protection is the same — documentation, a repository in your own account, and a handover you could give to someone else.