66 and 67 are indeed the only Regional trains with checked baggage. You don't have to ride those trains to check bags on them, so that helps with avoiding the ungodly schedules if desired. I have not had any problems the few times I've checked bags on Amtrak, but I've never checked golf clubs. AFAIK, there are no special areas for special items (except firearms). They all go into the same hollow baggage car, which is inaccessible to passengers on the train.

Would you be allowed onto the train with the clubs? It depends on how much else you're carrying on and what mood the Amtrak staff stationed at the boarding gates at BOS and WAS are in. I personally wouldn't try, but others might. Let's see what other responses you might get here.