It's really a 50/50 shot at getting the 2-1 Leather seats on the overnight regional these days. I commute on the northbound regional (#66) daily from PVD-BOS (along with 200 other commuters) and it has the "special seats" only about 50% of the time, unfortunately with no real pattern lately.

I would pay for Business class and hope for the best, but keep in mind you might be stuck in a normal coach with 2-2 seats. Even if you end up in a traditional business class car, you'll have a lot less people getting on/off throughout the night (I'm pretty sure they sell only the 16 seats the 2-1 seat car has, even when it's the bigger ~50 passenger car). You'll also get a curtain to block out the lights from outside the train.