How can I make non-disruptive backups of my instances and ebs?

Only data written to the disk is captured in the snapshot, data in memory not yet written to the disk will be excluded. For non-disruptive backups this is generally considered good enough.

You do have an option on Windows to do VSS snapshots that can handle open files a little better (https://docs.aws.amazon.com/AWSEC2/latest/WindowsGuide/application-consistent-snapshots.html)

If you need to make sure all data is written to disk first, the best way is to either shutdown the instance or unmount the volume being snapshotted.