I am going to buy Assassin's Creed Unity and Assassin's Creed Rogue, but the story is important to me. Which game, if either is next in the story line? Which should be played first? I am mainly talking about the story line in the present day.

I don't know about the present day, but apparently Rogue serves as a prequel to the past events in Unity, from what I've heard.

Pretty sure Unity is the farthest chronologically in the franchise. For the recent games it goes:

Black Flag then Rogue (I think, it may have some cross over with 3. Not picking it up until the PC version comes out), followed by 3 and then finally Unity.

Edit: Didn't notice the present day bit. In that case I don't know for sure cause I haven't gotten Rogue yet but I would bet that Unity would be farther along the story or at least more important to the current day story as it is the big next gen release while Rogue is last gen.