There were plenty of local outfits in Kampala when I went. I cant remember the name of the one I used, something boring like Uganda Safaris.
Make sure you get a birding guide for a day for Bwindi NP (where the apes are). I didnt see much on the gorilla trek itself - too busy crashing through undergrowth - but the place was heaving with jungle species.
I found the name of the one we used. It was
African Pearl Safaris [mailto:[email protected]]
Some bloke called Ben ran it.
They were fine. Not particularly cheap, but everything was as they said it would be, including the gorilla permits (most importantly). And the land rover didnt break down.