Are jolteons worth powering up for countering water pokemons?

It's excellent against Gyarados, one of the most common gym pokemon. This guy dances around Gyarados, dissing out massive damage.

Maybe, though there are other options like Dragonite or Victreebel or Slowbro with psychic attacks (against Vaporeon and other water type).

They are great against gyarados, and good against slowbro and lapras. I would use a plant type instead against vaporeon, since vaporeon's attacks would be weak to it while the plant's attacks would be strong against vaporeon. I have a jolteon powered up.

Jolteon is good but Riachu is the best electric Pokemon it's move set of spark and thunder and its higher base attack give it the highest dps of all electrics and joltions slightly higher hp and defence don't make up for it

Like they told you, Jolteon is really good against Gyarados and I have found it useful against Lapras as well, which is a nice thing.

Plus, I really enjoy using Jolteon in gym battles, he's so quick and fun to use.
Many purists will tell you that its not worth it, but imo, if you have enough dust, and if you get one with good IVs and Shock/Thunder, then go ahead. Its a fun 'mon really.

For other Water-type 'mons such as Vaporeons/Poliwraths I use Victreebel/Vileplume/Tangela. They kick ass.

No. Scaling is terrible on Jolteon you'll never get them high enough to deal with high level water types. To put it another way, Jolteon maxes out at around 2100 CP and has a lo subpar health pool. Vaporeon maxes at 2800 and has a huge healthpool. You're just not coming out of that matchup in a good position. They might fair better against Garydos (max 2600) but investing enough precious stardust to make a Jolteon useable for one matchup is kinda ridiculous. Get yourself one of the big 4 grasses; Exeggutor, Venusaur, Victreebel, Vileplum. IF you decide you really need to spend dust on an electric type (again I think this is a bad idea) Raichu is more serviceable.