Well I will start by saying you can’t go wrong with either and I have stayed at the Polynesian and the Yacht Club, Boardwalk, Swan and Dolphin more than once so I know the Epcot and Magic Kingdom area well.
I will start by saying the Polynesian is my favorite resort but I am not here to tell you what resort you should like better. I will just put out some facts to hopefully help you decide.
The Epcot resorts have so much to do around the lake so it is hard to beat the nightlife you can just walk right to. It is also a nice short walk to the World Showcase entrance which can be a plus. I like the Friendship boats to ride but when it comes to a transportation option they are extremely slow. Besides my complaint about traveling by boat the busses to those resorts can be frustrating especially at the Beach Club because it is the last stop after stopping at the Boardwalk, Swan, Dolphin and Yacht Club so you get off last and you try and get on a bus that may be full by the time it gets to your resort. Other than going to Epcot quite a bit of time or a rental car will be needed to get to other parks. With that said the resort is great and offers easy access to the other Epcot area resorts and its food and shopping.
Now out of all the Magic Kingdom resorts I like the theme of the Polynesian the best and its transportation options can’t be beat. It will save you time going to and coming back from parks and the resort offers so many fun things including one of the best kid programs, a dinner show and a pool that is right against a beach looking at the castle. So why do I think it has the best transportation and why is that so important? Well the time you waist getting to things is time you could have been enjoying parks or relaxing. Now you know how people’s perception does not always match facts. Well one misconception about the Polynesian is that it is only convenient to the Magic Kingdom. Well I did some time studies and you can’t argue with facts so I wrote a page about them. Here is a link for the full version but I will write some of the findings down here too.
http://www.tikimanpages.com/tiki/planning-quick/quick-getting-around
You see, Epcot is my favorite park but I actually prefer getting to it from the Polynesian rather than the Epcot Resorts. We often go in the summer where it is either hot or raining like Noah needs to build an arc soon. The walk from the Beach club is quick (timed at 5 minutes at a normal to slow adult pace). Now staying at the Yacht Club or Boardwalk is another 5 minutes or more. At the time I was staying at the Yacht Club so it was 10 minutes to the International Gateway entrance. Now keep in mind that usually you care about getting somewhere fast in the morning and in the morning Epcot is only open in Future World so the total time to get to the middle of the park was 17 minutes. Well leaving our room in the middle of the Polynesian and walking to the TTC to get on the monorail took 5 minutes. The ride is always the same timing (unless there is a hold up) of 8 minutes from TTC to Epcot on the monorail. To walk from the monorail to the same midpoint of the park took 4 minutes so both totals happen to come out to 17 minutes for me. Sounds like the Polynesian can be considered as convenient to Epcot as most of the Epcot resorts. Now throw this in as another factor. If it is hot out and you are pushing strollers would you rather spend 17 minutes pushing in the heat or spend half that time on an air conditioned monorail? Also in many cases we are running from rain storms. Would you rather be inside a monorail or running back to the Board Walk from Space Ship earth in a rain storm?
Well I see the Polynesian as a good location to easily get to the Magic Kingdom and Epcot and the busses to the other parks are not bad either. You also only share with either the Contemporary or Wilderness lodge depending on the time of the year and the Grand Floridian so you are second in line of 3 resorts. There is also an option of a direct boat to the Magic Kingdom.
To me all the resorts have great things about them so transportation is one of the big things that separates them for me and in my opinion no other resorts can beat the Polynesian. That being said I have stayed at most of the Disney resorts at one time or sometimes more than once.
The only other thing I see that is a major difference from the Polynesian and the BC is the room size. You have some of the largest standard rooms on property at the Polynesian.
Aloha
Steve
and "hanging" out there and taking the monorail.