We have stayed at the Polynesian 3 times and we stayed at the Beach Club this past July. Both are great. Here are a few points about both:
Polynesian:
The Hotel facilities are much nicer. More of a grand resort. The Island atmosphere and garden is very relaxing. The rooms are larger and nicer. The dressing area can be closed off with a door from the rest of the room. The Monorail is worth it. The view of the castle at nignt is nice + the nightly water parade is nice. The Pool is great - daughter loved the Lava Slide. Ohana's dinner is just ok. Character breakfast is good though. Kona Cafe is great. Laou is just OK.
Beach Club:
The Best Location at WDW bar none. The pool is the best at WDW bar none. Bus waits to MK, water parks, DT Disney seem to be a little long. Very large hotel, but you don't get the feeling of a grand resort. Don't get me wrong, it's very nice, but with what seemed like relatively low ceilings, it seem like just another hotel to me. Located just accross from the Board Walk which is really neat. Flying Fish - best meal at WDW. Rooms are just OK. Dressing area open to the rest of the room. Buffet at Cape May is very good. Close to Yachtsman Steakhouse which is very good.
You really can't go wrong with either place.