How do I know if an S3 bucket has been created by the Console or CloudFormation template

Take a look at AWS Resource Explorer. You can specify "s3:bucket" as the resource type and query for "tag.key:aws:cloudformation:stack-name".

If you have enabled CloudTrail logging for management events, you can identify who had created the bucket or any other resources from the logs. you can also get some help from the below link to query the cloudtrail logging: https://docs.aws.amazon.com/AmazonS3/latest/userguide/cloudtrail-request-identification.html