I'm a regular passenger on the Acela between NY and Boston because of the hassles of airport travel. And I've gone through the experience of travelling with my kids by air - starting with my daughter at 3 months. Lugging everything is an experience. But you'll need to lug it onto the train as well. The thrill of the train ride passes quickly, despite Amtrak's desire to market it as something special. As for the airfare - children 2 and older travel for the same fare as an adult, so long as they are accompanied by an adult. A higher fare would apply to an unaccompied minor (and no airline is taking a 2 year old without an adult). Children under 2 fly for free if they don't occupy a seat - and for 50% of the adult fare if they do occupy a seat. No offense, but I don't understand the logic of parents who wouldn't drive down the street without their kids strapped into a car seat, but are content to hold them unrestrained on an airplane shooting down the runway at a few hundred miles an hour. We paid full fare for my daughter when she was under 2, and were happy that the airlines had introduced the 50% fare by the time my son was born. Anyway, of all the things you mention, the only factor that seems significant is that you "don't fly well" - the other items will exist on the train, and just be more pronounced because it is a longer ride.

As for your original question - the Amtrak website can be difficult to navigate when trying to book accomodations. I took a look at the options for your travel dates, and it appears that there are only limited possibilities where accomodations are still available, and that on those trains where you can book upgraded travel you would have some or all of the following: long travel times (i.e. more than 24 hours), long layovers (even if all trains operate on time), and very expensive fares (i.e. well over $1,000 for the two of you, and perhaps over $2,000). You could fly first class for as low as $700 each and be there in 3 hours!!!!