We've stayed at both - BWI x3 and WL x2 - and we enjoy each of them for different reasons:
WL: Beautiful and relaxing lobby area, very much a retreat from the parks, wonderful to boat to/fro MK at the beginning and end of the day, Artist Point/Territory Lounge are so convenient (TL may be my favorite lounge at WDW) and the pool area is quite serene. Also, if you need CS, Roaring Forks has a great selection. On the other hand, we try to avoid bus transportation as much as possible, preferring to walk, boat or monorail. At WL, it's boat (yay!) to MK and bus to the rest. As a result, we stayed at WL more when we were always on the go and in the parks from morning until night - not as easy for us to take an afternoon break when staying there.
BWI: We love the atmosphere and theme, the BWI CL is my favorite of all the CLs we've tried so far, and the location on Crescent Lake is both peaceful and convenient to both Epcot and DHS. We love the ability to walk to Epcot and DHS (or boat if our youngest runs out of energy) and find the bus to MK and AK is just fine. A key reason we prefer BWI over WL is the proximity to all the Epcot dining and Epcot resort area dining for dinners in the evening. We're more likely to spend time in a park in the morning, return to the resort for a swim or boating break after lunch and then head to Epcot or around Epcot for dinner. We love the BWI quiet pool and the main pool is busy, but the slide is one of the best at WDW.
Really depends on your touring style and preferences, ages of kids, if any, etc. WL was great for us when we toured commando style and spent a lot of time at MK. BWI works better for us now that we take afternoon breaks and have so many ADRs in Epcot. Good luck with your decision!!!