When you pushed the baseball and bowling ball with an equal force, the baseball went farther on the table because it has a smaller mass. If gravity also exerts an equal force on the 2 balls, like your push, then why do they fall at equal speeds? 

The answer is that gravity doesn't exert equal forces on the 2 balls! It pulls down harder on the bowling ball than it does on the baseball. Suppose the bowling ball has 10 times the mass of the baseball. Then gravity will also exert 10 times the force on the bowling ball that it exerts on the baseball. The result is that the bowling ball is able to keep up with the baseball! The bowling ball may resist acceleration more than the baseball, but the increased gravitational force the bowling ball experience exactly compensates.