Stony Brook Company is a new vendor for me - I've just sent off an order for their William Deering museum-grade trowsers. They're the only vendor I know that seems to totally specialize in Federal trowsers. Even for museum-grade construction, the prices are pretty decent for authentic stuff.
The one thing that strikes me (and sold me) on Stony Brook is that the owner, Chris Sullivan is honest and up front about materials. He uses Woolrich material that matches up with the original cloth very closely. The only rub is that it's an 85/15% blend, but he has some great reasoning for using the material. I've read that his contruction is as close as it gets to an original pair, and a few avid reenactors on the Authentic Campaigner forums give his stuff a thumbs up. I say, if you can't tell from even a close inspection, then it's kosher. I can't wait for my pair of trowsers, and I'll post my opinion on them later on.