Capital City of Juneau.
If you rent your car at Anchorage, the cost would most likely less than you take your car onto Ferry.
Ferry fares are not cheap, even BC Ferry.
You should go to BC Ferry website and Alaska Marine Highways site to check out the schedules and fares tables before you set your mind on taking your car with you.
There are many sites on the web to help you explore Alaska. Just Google it.
Other than Anchorage, your best bets for accommodation would be bed and breakfast.
People tend to plan their Alaska trip (or Hawaii trip) many months in advance. However, if you can afford to just pick up and go, you can do last minutes thing and get better prices in cruise fares. However, it really depends on year such as in 2004 there were hardly any bargain, but in 2005 there were great sales for as late sailing as mid June, that popped up in late March/early April. But in 2004 there were plenty sales for Sept towards end of the season. In 2005, they were very hard to come by and some people actually received a bump for their sailings in late August/early Sept if they were flexible as cruiselines oversold. There is no pattern.
Generally speaking if you see a inclusive fare (cruise + port charges + tax) of $550 tp $600 for an inside cabin 7 day sailing on a newer ship, that is a very good fare. When I say inclusive fare, it means that is the total out of your pocket in order to get on board. Of course, you will still incur about $10 daily tipping, drinks, and the killer - shore excursions if you plan to take any.