Chuck,
I would tend to think that it would not work well for you in the family room. Unless your son is extremely short for his age, he would most likely be very uncomfortable in a 4'9" long bed. The two child's beds in the family room are only 4 feet 9 inches long. You can click
here to see a picture of the room, along with it's dimensions. Scroll down to the bottom.
I would suggest that you consider booking 2 standard bedrooms. I suspect that 2 standard rooms would only cost a little more than the family room. If you call Amtrak reservations, you should be able to get two bedrooms that are opposite each other. This would still allow you to look out both sides of the train, even though there would be a hall separating your rooms.
As far as window size, they are much larger than those found in an airplane. Plus each standard room has two side-by-side windows. The family room has windows on each side of the car.
While you can't just take any seat in one of the coach cars, you could ask for permission if you really wanted to sit back there. Additionally, you will spend some time in the diner for your meals, plus there is the Sightseer Lounge car.
The Sightseer Lounge has large almost floor to ceiling windows and is a great place to check out the scenery. Seating is first come, first served and is open to all passengers on the train.
Most people find that the meals are decent and adequate. Like any restaurant, it really depends on the staff. Some crews are better than others, but I've never really had terrible service or food. Note that all of your meals are included in the price of your sleeper tickets.
As for safe transportation, it's certainly safer than an airplane. Amtrak has a far better track record than just about any airline. If you mean safe, in terms of theft and the like, then again there are very few, if any problems. Just remember to never leave wallets or purses in your room if you are not there. You should also place out of sight, any cameras, video games, and other similar items.
You luggage overall should be quite safe. Access to the sleepers is restricted to passengers traveling in the sleeper. Coach passengers are not permitted to wander around in the sleepers. You can also lock your door at night or whenever you are in the room. There is no way to lock the door however, if you are not in the room.