My .02...or .25
The best way is with a disc harrow. I unintentionally killed three Timber Rattlers that way plowing a food plot one afternoon. Turned three snakes into nine. The next day, a Cottonmouth was basking next to the plow, and would not leave. Shot at him three times with a .45 Auto and missed all three times.
Two days later, while bush-hogging an area, I moved a piece of sheet metal so as not to run over it with the tractor, there were two Timber Rattlers under there. They got away before I could recover from it.
The next day after that, while cleaning beaver debris out of spillway pipe, Cottonmouth next to right leg. He was very territorial and didn't want to leave, shot at him with 9mm, hit him, but he flipped and flopped away hissing and spraying.
Cottonmouths are nasty, they have an anal gland that they will sometimes spray with, almost like a skunk, and it smells terrible. Occasionally, they can spray in a stream like a water gun.
So, there can be too many snakes in an area. At this location, there are planted crops, hardwood swamps, ponds, hog pens, planted pines, and clear-cut areas. It is infested with Rattlesnakes (Timber, Pigmy, and Diamondback) Cottonmouths, and Copperheads, as well as an Alligator here and there.
I don't look for them to kill them, but there are entirely too many there, and a bite from any of these in a rural area is in fact a LIFE THREATENING emergency. So if one is close to me in spite of my trying to be careful, I blast away.
They are in fact very hard to hit with a handgun bullet. I have sprayed entire magazines at them in the heat of the moment, to no avail.
Sticks and stones are fine, but be advised that a well fed four or five foot Cottonmouth is usually fairly stocky, and usually down right mean and nasty.
They will try to fight back with the stick, and that's usually how most folks get bitten by them is when trying to kill them with a stick or rock.
So if they are scarce in your area, it's probably good to leave them alone, but if there are too many of them they become a problem for your pets, live stock, and children that are not paying attention.
In that case, one cannot be frowned upon in my opinion for killing them when you can.
A shotgun is best if you have one handy, I have a short one just for that when I'm out and about on foot checking things out. My second choice is a .45 Colt with shot shells if I have any. Aside from those, whatever I have in the holster is better than nothing at all, but never a stick or rock.
This is good for a laugh or a shutter, depending on how you can visualize it. A friends wife had a Cottonmouth come into her ground blind with her at some point early in the morning. She shined her flashlight on it when she thought she detected some movement on the floor by her feet, and discovered it.
She then proceeded to stomp on it with her boots, and then cut it's head off with a knife!
My advice to him is to never make that girl angry with him, because she can obviously be meaner than a Water Moccasin.