Location, location, location.....
AKLodge is spectacular, but may not be worth the journey if using Disney transportation. Boma is very good, but not worth a hassle getting to/from resort-to-resort.
Cape May allows for a stroll along Boardwalk and/or into either Hollywood Studios or Epcot too.....which makes using Disney transportation back to your resort even easier.
If you are driving yourselves - AKLodge is spectacular and worth the trip to subsequently enjoy Boma. Start during daylight hours to enjoy the animals.