Hi Scarlett! Welcome to the forum.
My first thought is in agreement with what you have already stated, either ears or anal glands. Be sure to get in his ear and give it a sniff to see if you smell anything. It is important to clean your dog's ears after a swim so I am glad to hear you are doing that. Make sure you wipe them out too. Maybe after a swim you could hose Beau down quickly? What does he smell like? If he smells like concentrated poop then it probably is anal glands. If he smells like concentrated dog, then it could be that he is yeasty, maybe he doesn't dry off completely ever and the wetness under his coat is causing some funk. Maybe he's got yeasty paws. Some dogs stink just because of the kibble they eat. Maybe the shampoo you are using isn't completely rinsing out. I like to use one by Cloud Star called Buddy Wash. It's coconut based and makes my dogs shiny and smell delish. I don't use it often though. Perhaps your dog has a hormone imbalance, you'd need bloodwork done to check that. Sometimes a fish oil or coconut oil will help balance the body's fats. Yes dogs do sweat, I notice it mostly on their feet if they've been sweaty. We call it Frito Feet
Since you went to the vet and everything checked out, I would start with a fresh bath or at least a hose down, and let him dry completely before going back in the water. Then always make sure he gets a chance to completely dry. It sounds to me like it coincides with the swimming? I do notice when my guys play with other dogs and get slimed up, they smell funky too. Might just be something you'll have to deal with by hosing Beau off after he's done playing.
Good luck!