Most of the resources you mentioned are created as part of the Datomic system itself (not the ion tutorial specifically).
You can find information on deleting a Datomic system here:
https://docs.datomic.com/cloud/operation/deleting.html
In the tutorial, you created the API gateway manually, so that would not be removed by deleting the system. The lambda functions, s3 buckets, etc. are all managed by the Datomic system and you shouldn’t remove or alter them manually (see Deleting a System)