If you don't want to do the entire Inside Passage by AMHS ferry, try a day, or several day, trip to Juneau from the north. You can leave your RV in Skagway (?), Haines, Carcross, or even Whitehorse and drive your toad or TV to the ferry dock. Then leave your vehicle and just ride the ferry or take your vehicle on the ferry without the expense of paying for the RV too.
If you leave your vehicle in Skagway, you can take a fast ferry that gets you to Juneau in 3 hours for $165 RT/person, if you come back the same day. If you want to take your vehicle, you can ride the AMHS ferry for $100 RT/person and $222 RT/vehicle. A bicycle on the ferry is only $36 RT, so, if you want to ride around Juneau instead of drive, that's a cheaper option.
In addition, Juneau has a bus system that can pick you up and drop you off at the ferry dock. We rode the buses instead of renting a car after flying into Juneau and were even able to take a bus to Mendenhall Glacier.
And, while you are in Juneau, you can take a tour boat or AMHS ferry to Gustavus/Glacier Bay NP. It's only $66 RT/person via the AMHS ferry, but you will also have to pay to get to the Glacier Bay Hotel or the campground and for a tour boat in the bay. An 8-hour boat tour from Gustavus through the bay is about $215/person.
You can also take an overnight ferry from Skagway or Haines to Sitka. You can pay for a two-bunk cabin with a shower or just bring your sleeping bag and stake out a chaise lounge on the partially covered, heated (by heat lamp) rear deck, like many Alaskans and backpack travelers do. You can also sleep inside in a airport-lounge type chair on the forward observation deck, but you may not get much sleep. And, when you get to Sitka, there is a taxi-van shuttle service into town. Plus Sitka is small and easily walkable, so no toad, TV, or rental car is really needed.
So, there are options for seeing more of SE Alaska than you would merely from Skagway or Haines, without taking the entire Bellingham or Prince Rupert Inside Passage ferry route or even taking your RV on the ferry. It's not exactly cheap, but having the opportunity to visit Sitka (our favorite picture-postcard town in Alaska) is worth the effort. Imagine the sun setting over the Pacific Ocean behind a perfectly cone-shaped volcanic island just outside the harbor and more bald eagles than you can possibly count flying overhead and roosting on the Sitka spruce-covered tiny islets dotting the harbor. That's what you will remember if you take the time to take the ferry to Sitka!