Similar problem on my car, the stockers were blown to fuck (constantly open windows and dusty conditions isn't good for cars people! :upset
Now I've got old, but in decent shape, 80w replacements in there. At first any base made tons of noise, at first I thought maybe the mounting screws were loose (since you can only get them so tight without a helper) but after a couple days it's better :shrug: Bolts and screws are all still tight so I dunno.
If you take the covers off, it's real easy to shove foam, etc. in between the frame and the deck. Also possible that putting some sort of thin foam or rubber between the speakers themselves and where they mount would help a little.