Infantmom,
First, I highly recommend taking the suggestion of getting a redcap in Boston at South Station. This will help you with carrying everything and ensure that you can get your pick of seats.
Next, you will find that at one end of each car there is a set of seats where 4 people could sit facing each other, 2 & 2. You may want to consider sitting there so that you could place your baby in the car seat opposite you, instead of next to you. This could make it easier to attend to your baby and it would have your baby essentially facing backwards. That way in any abrupt stop, something unlikely to happen anyhow, the car seat would be stopped from moving by the seat cushion.
One drawback to this idea however is that if the train sells out, you will have company next to you & your baby.
If you don't opt for the above, then in a regular two seater, place the car carrier so that your baby faces the seat that they're sitting in. Again, this way if the train does stop suddenly, it will be the back of the carrier that hits the seat ahead of your baby. You can also try the bungee cord idea suggested by George, just be careful that you don't strap down the table tray on the back of your baby's seat. The person sitting behind you guys may want to use that tray.
Know that the general motion of the train isn't sufficient to bounce the carrier around. I can generally even leave my laptop safely sitting on the table tray without it being tossed off. And that's fare more unstable than a car carrier would be sitting on a cushioned seat.
Since you have two tickets, one for you and one for your baby, you are of course entitled to two seats. Had you only brought one ticket, then if the train had sold out, you would have no choice but to hold your baby. But with two tickets, the ball is in your court. You can hold him when you want, place him in the seat next to you if you want, or put him in the carrier in the seat next to you. And you can change things around as dictated by your needs & his.
Moving on, under no circumstances would I consider leaving the baby in the stroller, even if the crew would permit it and I think it unlikely that they will permit it. The brakes on the stroller simply aren't strong enough to keep it from moving in the case of an emergency stop.
Beyond that, sit back, relax, and enjoy your trip!