Jolteon, hands-down. First off, it's fast. The only pokemon in Leaf Green that's faster than Jolteon is Electrode (Aerodactyl's a notable tie). Secondly, it's strong with a solid base Special Attack. Jolteon can do a decent amount of damage to nearly everything in the game, plus it learns Thunder Wave at L42 so you can paralyze pokemon and use paralysis for catching if you wish.
Flareon, on the other hand, has a high attack stat that is difficult to use since Flareon learns next to no physical attacks. The only good non-Hidden Power physical attacks for Flareon that I can think of are Body Slam, Return, and Shadow Ball. All of these require you to burn a TM. Furthermore, Flareon is slow, and it's pretty vulnerable (low base HP, lower physical Defense, Special Defense is alright, but it won't help much against a water attack).
Lastly, Jolteon is useful not only immediately but also throughout the entire game. It can take out any Tentacool or Swimmers in the water routes, plus it can take out all of Lorelei's water pokemon in a single hit, deal a fair amount of damage against Bruno's fighters and Agatha's ghosts, and handle Lance's Gyarados with no problems at all. Flareon will work against Lorelei's Jynx. That's it.
Fire's simply not a very useful type; it's only good against Grass, Bug, and Ice, but most Ice types are also part Water, which ruins Flareon completely. Jolteon's good in-game, and it's a great subber in competitive battling, too. The only disadvantage is you'll have to teach it Thunderbolt by TM, while Flareon learns Flamethrower naturally... at L52.