The first thing to do is make sure you can explore them effectively.
If they are defined using SOAP or OpenAPI/Swagger then you're in luck - I've recently written a blog about how you can explore those with ZAP:
https://zaproxy.blogspot.com/2017/04/exploring-apis-with-zap.htmlIf they dont have any definition then you'll need to proxy a client through ZAP and explore them via actual use (application, regression tests, manual)
Once you have explored them then you can use the active scanner, but many of the rules are really aimed at web apps rather than APIs.
I'm hoping to address that in the near future.
You can also use manual features like the fuzzer.
Cheers,
Simon