I'd use a countersink if I had one. That's why I use a pedal axle. By the way, make sure you have the bottom of the crank braced with a small length of pipe that you should wedge between the bottom of the crank and the floor. This will transfer the shock of your strike to the floor and hopefully save the bb cups some damage.

You might soak some penetrant in the cotter if you're having trouble.

I once tried to tap tap tap the cotter out. Then I got mad and just whapped it with one Paul Bunyon strike. Bing! You'll feel so good when it's out.