Server.
But there are a couple of quirks to that answer you should understand.
Server has been around since 2003. Atlassian "hosted" arrived in 2006, but did not really start to become big until it was converted to "On Demand" in 2011 (renamed Cloud in 2014). Server had a huge head start on Cloud, and a lot of people on Server simply can't go to Cloud because their Server data is already too large.
Numbers 1: Atlassian could tell you exactly how many active Cloud licences there are. They could also tell you how many active server licences there are (although you don't know if some of them may be planning to leave and not renew). What they can't tell you is how many people have let their licences lapse, but continued to use the version they are on. The licence lets you continue to use Jira after it expires (without upgrades or support). I hear of one or two installations in that state every week.
Numbers 2: Do you care about unique instances or users? I've heard (don't quote me on this, because it's third hand) that the number of active Cloud systems is about the same as the number of Server installations currently actively maintained. However. Cloud instances can't go above 2,000 users, and the vast majority are 10 user systems, with most of the rest being under 100. I've worked on server instances that have user numbers in the tens of thousands (and a couple in the hundreds of thousands). Imagine the (main) bank I worked for - 1 instance, but the same number of users as 6,000 10-user Cloud instances.
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