Oh how I LOVE this question!
This is entirely a matter of opinion coming from the reader and there is no right or wrong answer. At least I always tell my students so.
However, based on the many times I've taught this story, Algy seems to be the most popular of the two.
Algernon is not supposed to be likeable: He lives above his means, lies, lives a double life, is excessive when he eats and spends, is upperclass without having the money, denies his help to his aunt when she needs him, and lives off other people's charities----but he does so QUITE happily.
That is probably why Algernon ends up winning this one: Because of his lack of shame, his embrace of excess, his funny and witty attitude, his ways to push buttons and to live life the way he prefers to.
Jack is not much different from Algy, except that he is less open about his double-life ways than Algy. Jack maintains a slight level of balance by keeping his money flow, by taking care of Cecily, and by disagreeing with some of the ideas of marriage that Algy shares (which, of course, are horrid).
I wouldn't say, however, that Jack is less likeable- But Algy has him won.
It is the opposing forces that make them friends. Algy is like Jack's open door to the city (literally, as that is when he goes to visit him as Earnest). Also, they balance each other: Algy's extravagance versus Jack's conservative ways to spend- Algy's delight in pleasure, versus Jack's moderation caring for Cecily. They are alike in that they have double lives that they have mysteriously only discovered at the beginning of the story, but then again, it was the polite Victorian Society and hypocrisy and secrecy were rampant then.