All the Disney Vacation Club resorts offer 2 bedroom villas which sleep up to 8. Some of them will have a master bedroom with king, bedroom with 2 queens and a pull out couch in the living room (I recommend Old Key West, they are HUGE). Some resorts' 2 bedroom villas will have master with king, bedroom with 1 queen and pullout couch, and additional pullout couch in living room. (some also have an additional sleeper chair, making them sleep 9 total)
Several of the DVC resorts (Old Key West, Saratoga Springs, Animal Kingdom Lodge, Bay Lake and Boardwalk) offer three bedroom grand villas, which sleep 12 or 13. The only ones with bunk beds are the tree house villas at Saratoga Springs. They also offer regular grand villas in the regular section of the resort.
All of those options (especially the grand villas) will be extremely pricey to reserve through Disney. If you really want to get a 2 or 3 bedroom villas I highly suggest renting points from a DVC owner.
All that said, by far your most economical option would be to get 2 regular rooms. You'd get more beds that way anyway. You could probably even get three rooms at a value resort for less than a 2bedroom villa would cost.