According to Destructoid, or perhaps more correctly their secret source, Take Two is tinkering with an MMO set in the Bioshock universe.
While this is by no means a confirmation, Take Two have shown that they consider Bioshock a franchise worthy of thorough exploitation, and they have also expressed an interest in the MMO segment.
Take it for what you will, but Rapture would be an interesting online world to explore... even if there has been nothing remotely massively online about the two first Bioshock titles.