How do I recover missing notes from iPhone and iCloud?

They may be in your last daily backup as FelipeV said, but you would have to restore your phone back to factory settings, stopping the automatic iCloud backup before it overwrites the old one. Then restore the backup.

If your Notes disappeared yesterday or before then yesterday's iCloud backup will have overwritten itself with no Notes.

I repeat, having phone-only Notes s well as iCloud sync'd notes is risky, to say the least.

If they were all in iCloud and they are not in Recently Deleted they they're gone.

However I am intrigued by your statement "and some of the ones in iCloud are missing as well." Because they should either all be in iCloud or all on the phone-only. You can't have both. Swapping iCloud on and off can easily make them disappear for ever.

They should be in a backup (if you did one). Did you? If not they are probably gone.