If org.eclipse.* imports in general are not recognized my first idea would be that you don't have a Plug-in project but a plain Java project. Do you have a META-INF/MANIFEST.MF file in you project? To use the DOT support in GEF4, import the org.eclipse.gef4.zest.dot.* bundles in the manifest. Then the snippet from http://wiki.eclipse.org/Zest/DOT#API should work. To check if GEF4 is actually installed, I'd try to open the Zest Graph View (see http://wiki.eclipse.org/Zest/DOT#GUI).
In general it is possible to develop SWT applications without having a plug-in project (see http://www.eclipse.org/swt/eclipse.php), but using a plug-in project makes handling the dependencies much easier. You can convert your plain Java project to a plug-in project in Eclipse (Right-click the project > Configure > Convert to Plug-in project). That basically just adds the manifest and should not interfere with the rest of the project.