Kittens can be taken from their mother without physical risk to their health as soon as they are weaned, which should be at about six weeks of age. The advice to wait longer is based on the idea that staying with mom and their siblings longer helps them to be better socialized pets. It may reduce behavior problems like play aggression because they learn from their family not to do that. But if it's a choice between learning to trust humans, so they could actually happily live as an indoor pet, or become fully socialized with their family, I think most people giving advice would agree that acclimating them to humans is better for them. The younger you can attempt to acclimate them, the more likely you'll succeed. Three months is already well past that key period where you'll be most likely to convince them to accept humans. Therefore, the best option, that will give them longest, healthiest life, is to attempt to catch them as soon as they are weaned, socialize them, and then home them as pets. 

If they are definitely too old to accept humans, then the most humane option is TNR or "trap-neuter-return." This is when you catch the cats in order to neuter or spay to prevent future kittens, then return them to where you caught them, so they can live out their lives in peace. 

There might be local groups willing to help you attempt to trap-neuter-return, so if you decide on this route, it's a good idea to see if such a thing exists in your area. If there are no such groups, then the safest way to catch them is to use live traps designed for catching but not harming cats. 

Since you live on a farm, there's a decent likelihood that if you removed all of your feral cats, new ones will discover your farm is now free of cats and move in, so having some neutered animals remain might also help in that way, besides also continuing their pest control services.