The train waits for a long time and is frequently stopped at the border for 3hrs+ (from experience.) Non US/Canadian citizens have to get off. I am pretty sure they wait for everyone to get processed because of the excessive time spent at the border.

The bus (which I have also taken probably close to 100 times) stop is much quicker. Everyone has to get off and go through immigrations/customs both ways. I have seen people get left behind at the border (though I don't know the reason.) The longest delay I have had at the border (delay as in we were waiting for people to get back on the bus, not a delay due to traffic at the border) was about 30 minutes or so. However, buses are a lot more frequent. From Toronto there can be 4 or 5 buses leaving between 7 and 10pm. If you miss one, you can probably take the next.

One thing about fares: the bus (~10h) is CHEAP. If you book in advance, it can be as little as $40 one way. The train is generally around $90+ one way and takes 12-14h. The plane can be as little as $90 one way or as much as $200 depending on the season / day of week etc.

I generally find the bus to be worth the savings. However, the train takes the whole day (no overnight option) and it's not even that cheap. So I either do bus or plane now depending on time constraints.