Join Date: Apr 2002
Location: Montréal (Québec)
A lot depends on the amount of time you have available. If you check at Via Rail Canada, basically all trains that take checked baggage handle bikes, which much be boxed in a relatively large box (that they provide for 20 $). Back to the original question, there are "transcontinental" trains from Halifax to Montréal, then from Montréal to Toronto (only the night train takes bikes if I remember correctly), then from Toronto to Vancouver via Edmonton.
If you have choice of direction (i.e. no specific end point), I would suggest flying to Vancouver, then riding to Edmonton, then taking the train to Toronto. That way, you'll take advantage of prevailing winds (a very slight advantage in the Rockies) and you'll do them as early as possible. I would recommend avoiding the Prairies unless you have lots of time available, and rather spend time cycling further East. From Toronto, you could cycle to Kingston, Ottawa, Montréal, Trois-Rivières, Québec, Rivière-du-Loup, Edmunston, St. John, Moncton and Halifax.