Either character can eat an infinite amount of enemies in the game, correct? So in a situation where there was a free-for-all eat fest (infinite enemies on an infinitely long stage) Yoshi's quick, long-reaching tongue would enable him to eat at a faster rate than Kirby. So if both characters played this imaginary infinite stage for x amount of time, Yoshi would be able to eat more.
However, if this infinite stage was flat and featured a constant stream of characters rushing at Our Two Heroes, depending on the speed and density of the stream, Kirby's vacuum may gain the upper palate because it can suck infinitely and suck in an unknown multiple of enemies at once. In this situation Yoshi may even be killed, again, depending on the speed and density of the enemy stream.
I go along with the first scenario because most in-game stage setups are the "Progress to the Right and Hunt" kind as opposed to "Stand Still and Kill" kind.
In summation, Yoshi's Tongue > Kirby's Vacuum