I had a similar problem in one of our bathrooms. It turned out that this toilet has an underlip (underneath of the top of the bowl, if that makes sense) that you really can't get to with a toilet brush. I have to use a cleanser with bleach and a paper towel and wipe up under the lip once or twice a week. But the pee smell is gone!
You can also go over the entire bathroom, including walls near the toilet and the floor, with Nature's Miracle, the product you use for pets. I use it on the wood floor in our breakfast area(where our elderly dog lives most of the time) about once a week. It really is pretty miraculous about getting out odors, and I'm pretty sensitive to smells.