Holliday is the better player, BUT until free agency begins we should be bending all our efforts to re-signing Bay anyway.
My reasoning is simple. We still have Jason Bay as a captive audience until free agency starts. It makes no sense at all not to make use of that. If he wants to test the waters and files for free agency, then the two are on equal standing and you should probably go more after Holliday. But don't ignore Bay even then, he's a huge asset in left field even if you accept the premise that Holliday's better.
Realistically I'd go hard after both. I don't think there's any particular reason to make the call as if we can only have one. Sure it's highly improbable to actually GET both players, but if you go hard after both the chance of getting at least one increases IMHO.
The worst case scenario here would be going after Holliday, losing him, going back after Bay, losing him. There's 29 other teams and many of them could use either guy and many of them have money to spend.
BTW I have a secondary reason for preferring Jason Bay. Bay is not a Boras client.