Curt, the Brown Pass campground is a sham. I've never camped there, and I only would as an alternate. Boulder, on the other hand, may be my favorite high campground in Glacier. It's pretty stunning, and it may have the best toilet-with-a-view in the Rockies. Brown, on the other hand, is a completely-treed in pass, and the campground is in the forest without much to show for all your work.
(Honestly, for anyone traveling over Brown Pass but not going toward Hole-in-the-Wall/Boulder, it's worth taking the trail at least half-a-mile to a mile or so that direction to get some of the more complete views of the area and down the length of Bowman Lake.)
Personally, I prefer the Stoney Indian Pass route too. The Northern Highline is fairly rugged because it has to avoid a number of cliff bands--you end up constantly ascending and descending, something like 3,000' gained and lost from Fifty Mountain to Granite Park. When you drop low, you can't see over Flattop Mountain to the main draw of the Livingston Range. The plus though is that its' secluded, has lots of wildlife, and the short detour to Ahern Pass is pretty phenomenal. Stoney Indian is one of my favorite passes--it's on par with Boulder easily. However, once you drop into the Belly River drainage, it gets brushy fast. That probably won't be as big an issue in September, but in July and August, the cow parsnip can completely cover the trail up to my chest (I'm 5'11"). Depending on the snow (which is high for us this year), it might be a week or two behind or it could be completely gone.
One alternate to think about (and my recommendation) is to go from Elizabeth Lake and over Red Gap Pass. It's another less-traveled area, and I really enjoy it a lot. When you get to Many, you'd have to walk or hitch a couple of miles to the Swiftcurrent Motor Inn, but that shouldn't be too big of a problem if you have a pack on your back and trail dirt to show for it. People are pretty willing to give you a ride if necessary.