Hi and welcome!
I am sorry about your surprise. Some sows, especially with a single baby will hardly show. I got caught out with my first adult piggies by the fact that guinea pigs are not separated into genders on the several days transport from rodent farms on the Continent to the shops over here.
Please be aware that boars start as early as 3-5 weeks old. That is why we recommend to separate them at 3 weeks old/ ca. 250g of weight, which is the average weight for that age. Separate earlier if he is over 250g well before the cut off date or leave him for a week longer if he is well below. Weaning is well under way by three weeks old, so he is not missing out on much.
You may find this information thread from our Pregnancy, Baby Care and Sexing section helpful:
http://www.theguineapigforum.co.uk/threads/separating-baby-boars-and-rehoming-babies.109391/
The thread also contains a link to the best sexing website, but you are always welcome to post a preferably clear picture of the relevant parts in that section for a second opinion.
If you want to hang onto your boy, you have two choices. You can pair him up with another character compatible boy, preferably at one of our recommended good standard guinea pig rescues (your closest is Wood Green by Godmanchester, which offers boar dating under expert supervision at the rescue) and preferably older so they have a better chance of making it when your little one hits the big teenage hormones. That means that he will never be able to live with mum and auntie, but he will have an uncle pig to take him on and socialise him at a time when he desperately needs company. The boars will need to live out of sight and reach of pheromones from the sows, either at a little distance or above the sows.
The pet shop you have got your piggies from should provide you with an adequate 2x4 ft cage.
http://www.woodgreen.org.uk/about/visit_us/godmanchester
https://www.facebook.com/WoodGreenTheAnimalsCharity
The other option is neutering. However, you have to wait until your boy is physically well developed for an op (about 4-6 months old; his testicles need to have descended). You also need to have a piggy savvy vet with a good track record in piggy neutering, as especially post op complications like abscesses are otherwise quite common. The mortality rate has thankfully come down a lot in the last few years. Here is our piggy savvy vets locator:
http://www.theguineapigforum.co.uk/pages/guinea-pig-vet-locator/
Thirdly, you need to factor in a 6 weeks post op wait until your little boy is 100% safe to join your ladies. I have the baby from a supposedly safe over 5 weeks post op boar living with me, just to make that particular point! During this long wait, your little boy has to live next to mum and auntie, but he will not be allowed to share the same space at the same time. Impregnation only takes seconds, and you will not be quick enough to prevent it even when supervising!
Various members with single boar babies have gone down either way successfully. You have to weigh up the pros and cons for you and your specific situation.