Deactivating an API, one step at a time (via) Bruno Pedro describes a sensible approach for web API deprecation, using API keys to first block new users from using the old API, then track which existing users are depending on the old version and reaching out to them with a sunset period.
The only suggestion I'd add is to implement API brownouts - short periods of time where the deprecated API returns errors, several months before the final deprecation. This can help give users who don't read emails from you notice that they need to pay attention before their integration breaks entirely.
I've seen GitHub use this brownout technique successfully several times over the last few years - here's one example.
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