It depends on the situation. In an open field, I'd say the musketeers have an advantage. Its where they're supposed to fight.
In woods or broken ground, though, I'd say the archers have a strong advantage.

But the muskets main advantage over the bow is numbers. You can train a man to fire a musket without shooting his own foot off in a day. Training an archer takes a looooooooooot longer. And a longbow is probably quite a bit more difficult and time consuming to make than a musket.
So really, its not a question of 100 men with bows vs. 100 men with muskets, but 100 men with bows vs. 1000 men with muskets.

Muskets have other advantages as well. Bayonets, the ability to fire prone (although reloading is a different matter), durability, and getting wet wont permanently damage them.