Photo Stream how-to: Delete once, remove all copies
When I take a picture with my new iPhone 6, a copy immediately lands on my other iPhone 5, my iPad, my MacBook Pro, and my iMac. But if I want to delete that picture, I must delete it separately on all five devices. How can I delete a picture on all devices with one action
The short answer: Be patient.
The longer answer: Photo Stream was built to sync photo additions as well as deletions on all devices associated with your iCloud account. So, when you launch Photos on your iPhone 6, go into your photo stream, select an image, and then delete it, it will eventually disappear from your other devices provided that they're connected to a Wi-Fi or Ethernet connection.
There are cases when this won't happen, however. For example, if you've moved any of these images to your Camera Roll on an iOS device or imported them to an iPhoto or Aperture library, they'll no longer disappear when you delete them on another device because these copies are now part of another album.
Also, if the image is more than 30 days old and you have fewer than 1,000 images in your My Photo Stream album they may remain.