Near the end of Bioshock Infinite you go through a "tear" to Rapture. Everything in the area looks fairly newish, but there's nobody there (and there's a "big daddy" suit in one of the halls). Was this before or after the other two Bioshock games?
The game is intentionally vague and non-specific about when, and what version, of Rapture Elizabeth takes Booker to in Bioshock: Infinite. Since Elizabeth can travel to alternate dimensions, we don't even know for sure, in this version of Rapture, that Andrew Ryan even exists, let alone if there will be a civil war between himself and Fontaine. There's certainly none of the expected propganda of either person in that version of Rapture, or any indication that there's any kind of war brewing, happening, or recently ended.
There is also some evidence that this version of Booker may himself be a parallel version of Andrew Ryan, since Booker is able to use the bathyspheres that are genetically coded to Ryan's DNA, which would mean he must have visited at some point before the civil war, when Ryan was still alive and freely wandering around Rapture, but that's pretty heavily speculative.
Note that the Burial at Sea Episode 1 DLC has a much clearer place in the Bioshock 1/2 timeline: it specifically happens in the same city as Bioshock 1 a year before the civil war breaks out. However, the Booker/Elizabeth from Burial at Sea are just two more parallel versions of those characters from Infinite, so that doesn't really help us place the original foray into Rapture any better.