CP,
You can't get seat assignments for Acela, even in First Class. When Acela first came online, it was possible to select your seat. However that program died a quick death, since passengers complained when they were asked to get out of a seat that they weren't assigned to, attendants and conductors refused to enforce the seat assignments, and a program for electronic ticket collection went belly up.
So seat assignments are first come first serve.
As for other advice, make sure that you take advantage of the Club Acela Lounge in NY and if you are returning from Boston via Acela in First Class and are boarding at South Station, then again you can take advantage of the Club Acela Lounge.
In Boston, you'll be escorted to the train before the general boarding begins. Sadly in NY that luxury does not exist, but generaly they do announce the track number inside the lounge before they announce and post it outside in the main station. So if you don't dilly dally, you can usually be at the head of the line at the top of the escalator.
Or if you know Penn well, then there are other ways to beat the line.
