I would say that more often than not the samurai wins, largely because I don't think a battle between the two would ever come down to a swordfight, even with the restriction on firearms.

In addition to the various swords (most notably the katana) that we typically associate with samurai, samurai also had access to bows and arrows, which means they could quickly engage in long-range combat if necessary (in fact, the earliest samurai were masters of the bow).

A musketeer was typically armed with a sword (usually a rapier), a dagger (usually a gauche), a firearm, and maybe a grenade or two.  Take the firearm away and the musketeer's long-range attacks are limited to grenades, assuming that he was even carrying them to begin with.

I believe that an arrow can be launched from a bow in a smoother and quicker fashion than a grenade can be thrown and detonated, and because of that, the samurai has the edge at long-range combat, and thus the battle as well.