Aloha! The Polynesian is such a lavishly themed hotel with its lush gardens and tropical feel. Also, the room were renovated not too long ago, so you will be able to enjoy all the new furnishings when you visit this fall.
Hmm, the best longhouse (building) may depend on what you prefer most. Tuvalu, Hawaii, and Tahiti have the best water views. Hawaii and Samoa are near the volcano pool and the boat launch. Tonga, Samoa, Niue, and Rarotonga are near the Great Ceremonial House, which has the shops, restaurants, and monorail loading area. Rapa Nui is close to the Ticket and Transportation Center, so it is easy to walk to the both the Magic Kingdom monorail and Epcot monorail.
If this seems a bit overwhelming, I'd like to suggest looking at a website called tikiman2001.homestead.com which is created by a loyal fan of the Polynesian resort. It is filled with many, many photos and further details on each of the longhouses.