According to a new job listing on Gamasutra from 2K Boston, their upcoming sequel, BioShock 2: Sea of Dreams, will indeed have multiplayer as they are looking for a Lead Multiplayer Designer and Lead Multiplayer Engineer on an upcoming “AAA” game. The listing expects that “you to be familiar with BioShock” as well as other Irrational products.
Considering that 2K Boston has no other announced projects in development, we’d say this is for BioShock 2.