Some pros and cons...
The rooms at the Polynesian feel substantially larger than the Y/BC rooms.
The bathrooms at the Polynesian don't have the split plan, the sink is in teh same room with the toilet and shower.
All Polynesian rooms have a daybed that is a standard twin, so very comfy for all but very tall or large guests.
Not all Y/BC rooms have day beds. Some of the day beds are smaller than a standard twin, more like a loveseat in length.
All Y/BC rooms have the split bathroom with the sinks in a dressing area outside.
All YC rooms have a full balcony.
99% of BC rooms have a balcony, but only half are full, some are small standing only balconies.
About 25% of Polynesian rooms have no balcony at all.
You can walk to Epcot and MGM from the Y/BC. You take a bus for AK and MK.
You can take a monorail to the MK and Epcot from the Polynesian. You take a bus to AK and MGM. (I personally think that the monorail to Epcot from the GF/PR/CR is a long process and I'd prefer a direct bus, JMHO)
At the Polynesian you will find three dining options, Ohana which is almost impossible to get into without an ADR, the Kona Cafe, and Captain Cooks counter service. You can take a 10-15 minute walk to the GF for fins dining at V&A's or Citrico's, as well as Narcooses which is probably the most family friendly of the WDW Signature restaurants. There is also 1900 Park Fare which usually requires an ADR and the GF Cafe, plus a counter service restaurant. A quick monorail ride takes you to the MK or Contemporary for additional dining.
At the Y/BC you'll find fine dining at the Yachtsman Steakhouse, family dining at the Yacht Club Galley, an old fashioned ice cream shoppe atmosphere at Beaches and Cream, and some "counter service" at the gift shop at the BC and the pool bar. A five minute walk to Epcot gives you ESPN, the Big River Brewing Company, the Flying Fish, Spoodles, and the Boardwalk Bakery. At the Swan and Dolphin you'll find another six or seven restuarants including Blue Zoo (fantastic upscale!), and a place to get Starbucks in the morning. You can also walk into Epcot and have all of the world showcase restaurants available.
One nice thing about the Y/BC is that it's all self-contained under one roof. At the Polynesian, if the weather is bad you're going to get drenched. At the Y/BC you can get to the lobby or restaurants without getting wet. That's something to keep in mind.
SAB is a fantastic pool, the main pool at the Polynesian is nice, but I love the lazy river, and they don't ahve one of those. Both get jam packed during the warmer months.
Any of them is a great choice, and I'd think about which park you are planning on spending the most time in.