It may be related to perspective that you are in? What is the perspective? Can you attach a screenshot?
Try to use "Project Explorer View": press Ctrl+3, then type 'Project E' and select the view from the list.
Now in context menu on plugins folder you should see "Install Cordova Plug-in" in the middle.
Well, I started Eclipse to get a screenshot and though I'd do a right click on plugins to show that "Install Cordova Plugin" wasn't there and guess what? It was there! But I swear it wasn't there yesterday and the only update I have made was the Android tools.
Thanks for taking the time anyway.