Did you enable this checkbox in iPhoto's Photo Stream preference pane?
If you did that your iPhoto library uploaded the maximum photos that can be added to the PS.
Uncheck that box, go into Photo Stream in iPhoto, select those photos you don't want in the PS, Control (right)-click and choose Delete from Photo Stream.
That will drop you below the 1000 limit. This Apple document discribes the limits of PS: iCloud: Photo Stream limits