Andrew, I have family in Homer (our only grandkids), and have visited Alaska 9 out of the last 12 years. There is no one "best" way. Just what sounds good to you and your wallet.
I would get the "Alaska state planner" and the "Milepost Magazine" (any bookstore)for a start to see what type of trip you want. The first few years we mostly flew into Anchorage and rented an RV. Lots of freedom to go where you want and stay for how ever long you can.
We did the "cruse" through the inside passage once, because we got to see many places you can't get to by land only. We went on the "World Explorer" www/wecruise.com a small to med size ship that I would highly recommend. Holds about 700 people. You can also use the Alaska State Ferry system, but must plan way ahead for that.
Use eye shades to sleep. Most drugstores in Alaskas carry a good cheep supply.
We also used many B&B's. They are 100 times better than the hotels and much cheeper also. Finding them on the internet is easy.
Good luck

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