TLDR; Anything but Water Pulse.
Vaporeon is still going to play a big part of the current meta. It has the 7th highest CP, and it’s really easy to get.
The highest damage moveset is Hydro Pump (Water Gun is the only quick move). This has a damage-over-time of 21.6.
Aqua Tail comes in close with a DoT of 19.9. This is 3 bars, so you can cast it more often. After some gym battling so far, I find Aqua Tail harder to dodge. Especially with my super slow Venusaur.
The ideal counter to Vaporeon is Dragonite with Dragon Tail / Outrage, with an advantage of 19.6. Not because of type advantage, but sheer volume of damage.
The next best counter, which everyone should hopefully have by now, is Venusaur with Vine Whip and Solar Beam, with an advantage of 18.3.
Coming up in 3rd place is Exeggutor with Bullet Seed and Solar Beam, with an advantage of 17.6. Finally, Exeggutor has dual grass moves! Sadly, Bullet Seed DoT is awful.
One could argue that Bullet Seed has great EPS, which boosts the DoT of Solar Beam. And Exeggutor has a great attack base stat of 233. Plus, Exeggutor has more HP than Venusaur. And it’s more common.
While all of that is true, Venusaur is still slightly more efficient at trading damage with Vaporeon. Venusaur has better defense so you’re not chugging potions. And most should have Venusaur by now. It’s your call though.
As a defender, Aqua Tail is definitely the most annoying.
As an attacker, Hydro Pump does slightly more damage. But Aqua Tail has better weave, and less overkill. So it depends on your play style.
To counter, keep using your Venusaur. You could train up Exeggutor if you don’t have Venusaur already, which is a good option too.