I have both guns, but in percussion. The Trapper is the more accurate of the two. It's easily as accurate as the T/C Patriot, which is essentially a target gun.
In flinters I hear a lot of praises for Lyman's locks, but I hear cursing at Traditions' locks. As much as I like my percussion Trapper, if I was in the market for a flintlock pistol, I think I'd be far more tempted to choose the Lyman.
I guess it would depend on what you wanted the pistol for. For target shooting, I think the Trapper might be the better choice. If the lock gives any problems, I'm sure it could be tinkered with and tuned to work fine. For hunting, the Lyman might be a better choice.