There are two things you can try.
Option 1: Remove restrictions
Step 1: Go to the GitHub Organization settings page and click "Third-party access"
Step 2: Click "Remove restrictions"
Option 2: Selective access
Step 1: Revoke Snyk access from https://github.com/settings/applications
Step 2: Visit https://app.snyk.io/auth/github-upgrade and click "Grant permissions"
Step 3: Click "Grant" next to the GitHub Organization(s) you wish to allow access to Snyk