Sorry its taken so long to write this up.
Where to start. OK, first thing is first Vancouver airport doesnt have fantastic transit with the main city, your a year early! Buses and Taxi's are your best bet, but there wont be a tube until next year. Vancouver downtown is fairly small by US standards and much more dense than a US city. The blocks are smaller so walking two-three blocks takes minutes, very different to somewhere like LA.
Downtown, if your looking to stay somewhere, but make sure you don't stay in the 'West Hastings area' of the city. Its rough and full of down and outs. Vancouver has a real problem here and they are slowly trying to sort it out. Expect the news to be plastered with this in 2010 when we have the Winter Olympics. The area to avoid is East of Richards and North of Georgia.
Downtown area is great to stay if your backpacking around as everything goes from there. Other areas would be Kitsilano (more trendy) or South Granville ( near Broadway on a map). Personally all our friends have staid downtown when there backpacking. There is quite a bit to do here as well. If your adventurous, then you have Diving,Caboeing, biking etc as well as the usual touristy stuff. We have three mountains immediately north of Vancouver, so you can go mountain biking and tr eking. Further North, Whister offers lots of summer activities as well. Lots to see sightseeing wise as well. Vancouver has a great (but not really big) Aquarium. Old City (Gastown), Stanley Park, Capilano Suspension Bridge, Granville Island, Science World (from Expo) plus others. The only things that aren't really worth it are the Space Centre (for kids) and the Zoo (which isn't in Vancouver!)
If you have more time, you should look at going to the Okanagan and the Rockies. You can take a train here, or drive. Simply Stunning. We went to the Rockies and spent a few days there and it was magical. You can also visit a massive glacier (Columbia Icefields) in the summer which is 1000's of years old.
Re you questions. Ferry - The ferry doesnt stop at Vancouver. I dont believe there are any ferries, only curise ships, which are expensive. Its quite amazing
Immigration - Canadians will ask you where your staying, what your doing and give you a bit of grief. Just have your trip planned out in your head and have addresses ready. They love addresses. Other than that, its easy! US - going into the US you will need to fill out a green form which gives you 90 days as a visitor in the US. Once you have it, then you just show it each time you cross the border. Again, know what your doing etc. You obviously need your passport! If your on a bus, coach or train its no different you still have to show the green visa and passport. I went on a coach to Seattle last year to import my car. Everyone had to depart the coach, queue up at customs, show (or get) the paperwork, then back on the coach. Slow, but not that painful really. You'll find longer line ups at this side (US is cheaper for shopping so lots of people venture down south in the morning)
One thing with the borders, you cant do hire cars one-way. Some hire car companies will not let you taken a car over the border and then back, but IIRC Canadian divisions are more relaxed about this so double check if your thinking about it.
I would recommend the train from the Pacific Coast (which is near the downtown core) or a bus. There is a coach that goes from Vancouver-Seattle and stops in Bellingham as well as Seattle and SETAC. The coach starts in downtown Van and is the one I used when I imported the car http://www.quickcoach.com/
its cheaper than train, but not as fast or fun! Coach is more frequent (although do allow for delays at the border)
Mountain bikes on trains - yes, I'm pretty sure they do. The skytrain also allows them at non-peak times. Almost all buses in Vancouver area have bike carriers on the front, so you could get a bus from airport with your bike.
Anyway, I'm ure you have lots of questions, so fire them my way. While we've been here, we have also been to Portland (v nice), Seattle (similar to Vancouver), Canadian Rockies, Okanagan, LA (didnt like!) and San Fransisco (fantastic) if you have any questions. We actually made a 2 week holiday last year driving down the coast to SF, staying there a few days and then working our way back up through Sacremeto, Nappa Valley, Crater Lake (Stunning), Columbian River Gorge and back.
drop me a line, I'll answer quicker next time :)