Hi Lindsay,
Thank you so much for visiting the Disney Parks Moms Panel with your question. You are deciding between two beautiful resorts.
Disney's Wilderness Lodge has a relaxing Pacific Northwest National Park feel.
Disney's Polynesian Resort transports you to the South Pacific islands. Both are amazing.
It sounds to me like the most important detail for you in choosing your resort is ease of transportation to theme parks with your little ones. Given that, I would recommend Disney's Polynesian Resort. You are right - Disney's Wilderness Lodge will typically cost less than Disney's Polynesian Resort; however, the convenience of being right on the monorail line at Disney's Polynesian Resort cannot be overlooked. You will be able to get to Magic Kingdom and Epcot using the monorail from Disney's Polynesian Resort. From Disney's Wilderness Lodge, you would take a boat or bus to Magic Kingdom and a bus to Epcot, both of which will take significantly longer than the monorail. From either resort, you would take a bus to Disney's Hollywood Studios or Disney's Animal Kingdom, so those will be about the same.
I hope that these thoughts help, Lindsay! Have a great time planning your vacation, and please do not hesitate to ask if you have any further questions.