People often ask me if there's a difference between having boy guinea pigs as pets or having girl guinea pigs as pets. There are a few differences, and I can't say there's one answer of which make a better pet.
Boys
I find boys are often a bit more bold than girls. Probably related to higher testosterone. But every guinea pig has his or her own unique personality and plenty of my girls are bold and pushy.
Boys, especially those that are older or less active, may need their anal sac cleaned periodically. It's related to their muscles in that area which is why older, overweight, or less active guinea pigs are more prone to get a build up here. The build up is usually white, off-white (yellow or tan or greenish) in color and smells just horrible. Usually you don't notice any smell even if there is build up because it's inside their body, but when you clean it, you will smell it and it's so bad. The good news is it's easy to clean a boy's anal sac. Most videos online demonstrate doing it with a Q-tip but I don’t like putting anything up in there, so I use gentle massage under warm running water in my bathroom sink to gently express the area, loosen the build up and carefully remove it with my finger tips. You can either wear disposable rubber gloves, or you can wash the substance off of your hands very easily just with soap and water. For boys that have had this problem before or those that are in a higher risk category to get build up or impaction, they should be checked every week or every other week and may need cleaning that often, or may need it much less frequently. That's the down and dirty about boys.
Girls
Girls aren't all sunshine and rainbows either though. To start with, they go into heat about once every 2 weeks and for that time (which typically lasts ~48 hours) they can be cranky and grouchy. Piggy PMS so to speak. It also took me a while to figure out why the sides of my guinea pig cages were getting gross so fast, and I finally realized my girls often do sort of a "straight backwards" spray of pee. So with girls you may need to clean the sides of your cage more often and if the solid part of your cage is short, they may get a fine mist of urine on your walls or whatever is next to the cage. Not very "ladylike"!
I don't think there's a really strong reason to get guinea pigs of one gender or the other for pets. It really comes down to personal preference and which guinea pigs you fall in love with. :)