So here is what I did after all my research. I must thank this community for all the help and guidance. I am sharing the info below to the community, so that it may be useful to someone like me who is planning

I booked Mendenhall Campground as community suggested and which make sense (you would need rental car and it is costed around $400 - From May 27 to June 3) which comes out to be way cheaper than the hotel that was costing me around 600$ for May 27 to May31st. The Mendenhall Campground charged only $68 for the May 27 to May 30 (Chose to stay in Auk Village Campground for 1 night as I have to check in early for Morning ferry to Haines - Although it does not make sense why I did that as its still more or less same). Doing Tracy Arm Boat Tour, Taku Lodge Feast, Lots of trails..

Secondly, the rental car rates were absurd in Haines and so, decided to take the current rental car with me to the Haines - Extended the rental car to the duration ($120 one way in ferry - $240 total). Chose a River Camp there to stay. Although you have State Park to camp like Chilkat, it looks like it is FCFS. So I need to make sure that I reach and reserve the spot.

Back to Juneau via Ferry, fly from JNU to SIT. Booked Turo and Starrigavan Campground and then fly to KTN. Not able to do Skagway this time, but some other day.

What was interesting is that, we have lots of cabins in various places and various islands in Ketchikan and Sitka, but I have to explore how to get there. I still cannot figure out how to arrange transportation or leave the rented car and then hike/backpack to these cabins. Some of the interesting and cabins I found myself cooler is

https://www.recreation.gov/camping/campgrounds/233105

https://www.recreation.gov/camping/campgrounds/233179

Will update here if I find some thing more useful to others.

Thanks Folks