Something nobody here mentioned was Serana's comment on the Dwemer, who supposedly vanished in 1E, 700. She is surprised that they'd let their cities get so run down.
As mentioned multiple times the dragons still existed when Valerica left. Durnehviir being all the proof you need of that.
From the timeline:
Serana asks you who Skyrim's current high king is when you free her. Harkon has a dragon presit dagger in his room. I'm wondering if Harkon might have been a dragon presist or affiliated with them.
There's also the bits about Serana mentioning the Volkahar castle having previous owners and there being ancient nordic skeletons walking around outside. She mentions that the nordic tomns were old even when she was around. Them being from the merithic era stll gives this theory some room to work with.
"I was always taught to avoid these types of ruins. I think I see why, now."
"Nordic ruins. Even older than I am. I wonder if the draugr are as gullible as they were when I was a girl."
From above
"1E 105
Lamae Beolfag becomes the first Vampire in Tamrielic history"
That Serana is fromt he merethic era theory instantly goes out the window. But Harkon does say his clan are some of the oldest vampires in Skyrim.
"As you know, vampires are powerful, but we have limits. Our great enemy is the sun, and until recently it's an enemy we've had no way to fight.
For centuries I searched for an answer to this problem. I found an old prophecy written by a Moth Priest" - Harkon
From another wiki page: The Falmer made their pact with the Dwemer in the merethic era. Giving them time to devolve and attack the chantry. Vyrthur created the prophecy some time after. There's wiggle room between 1E 105 to 1E 145 and beyond that Harkon could be a king with the power to sacrtifice 1,000 innocents. If he saw his way of life coming to an end as well as being an aging mortal man, he could become a vampire, seek a solution to the daylight problem and discover the prophecy before 1E 700 when the Dwemer vanished. Serana would be familiar with the Dwemer and their cities, the dragons would still be around for Durnehviir to make a pact with the ideal masters against Valerica. Serana mentioned that she spent a good deal of time at the castle as well I believe.
So based on all the info I've seen, I'm assuming Harkon was from the early first era. In the first couple hundred years and maybe around 1E 300 - 699 had gone mad, Valerica had left and sealed Serana away. At whatever the latest point that Durnehviir and other dragons might still be around but would also see the need to find a way to maintain his superiority.
There's also the quote above of Serana mentioning she was locked away in the first era as well as the website linked above where it was mentioned that she was locked away int he first era. All evidence at least supports it being before 1E 700.