I've done it booking directly through VIA rail. However, I used to live 10 blocks from one of their offices. I would suggest using a
travel agent.
It was a great experience to do once. I booked a berth, which was half the price of a cabin, but still included the 1st class dome car and all the meals. If you can handle just a curtain for privacy, it's a great deal.
Train travel between Toronto and Vancouver is very slow. We left Toronto in the morning, and stared at nothing but rocks, trees and lakes until mid-morning on the third day. I loved the prairies, where you can see for miles and miles, but most of our fellow travelers muttered something about it being boring and left the dome car. The trip through the mountains is spectacular, but much of the journey is at night. The prairies give way to the mountains in late-afternoon of the fourth day, and you arrive in Vancouver on the morning of the fifth day.
To see the most of the mountains (the highlight of the journey), make reservations close to the longest days of the year or around a full moon, and plan to spend most of your time in the dome car.
Another noteworthy caution is that the Vancouver train station is on the fringe of a bad neighborhood. While the SkyTrain is very convenient to get from the train station to downtown and the port, you do have to cross a 200 yard gauntlet of homeless panhandlers. A taxi from the train station to the port is brief and likely $15 or less.