My first thought was the second, but thinking about it I think the first would cover a whole line of chairs that the second leaves kind of unmentioned. It could also be taken to mean that there were two groups of chairs with a space between the groups. However, I might amend the first to read:

There is a space between each pair of chairs.

But really, without some context any way you say it could be misconstrued. Context, like redundancy, is our friend.