Raine gave birth to a child around 17 Years before the main events of the game begin. We can determine this because Rinoa is 17 years old and that her mother (Julia Heartilly) married General Caraway some time after Laguna went away to war, being later wounded and nursed back to health in a town called Winhill under the care of Raine. It is while in Winhill that Laguna learns that Julia has gotten married. Being that Squall is also 17, it must have been around this same time that Squall was born, and in light of the fact that Laguna and Raine got married, and the rest of the evidence that follows, that Squall is Laguna's son is not only well-supported, but can't logically be anything but fact.
Consider that Raine had wanted Laguna with her when she had her child:
Ellone: You can't change the past. I just found that out. When I was kidnapped, Uncle Laguna went on a journey to find me... But because he did, Uncle Laguna wasn't able to be by Raine's side when she died.
Raine wanted to show Laguna her new born baby... Raine kept calling out
for Laguna. So no matter what, I wanted Laguna to stay in the village...
Aside from the obvious fact that Raine would have wanted Laguna to be there at the birth of her child if he were the father, there's also the fact that when Raine dies, Ellone is sent to Edea's Orphanage. Logically the child she had just given birth to would have also been sent to the Orphanage, and Squall is with Ellone there.
The Tutorial section of the game states the following about Moombas: "A mutation of some unknown animal. Details are unclear. Remembers people by licking their blood." Upon tasting Squall's blood, the Moombas in the Galbadian Desert Prison think that he is Laguna and begin addressing him as such, meaning that his blood tastes the same as Laguna's. This would not occur without there being a genetic similarity in their blood.
When trying to speak to Ward on the Ragnarok, Kiros tells Squall "(Ward says... Good thing you don't look like your father.)" When speaking to Kiros directly, he says "You look very much like your mother." Kiros would have needed to know or at least have sen Squall's and known they were his parents in order to make such a comparison. Kiros knew both Raine and Laguna.
Also, when speaking to Laguna while on the Ragnarok, he will say "Let's talk when this is all done. I have a lot to tell you... Well, if you don't want to hear it, I'll understand," implying that he wanted to discuss something important with Squall, but knew he may not take it well. Being that Laguna knew Squall considered him a silly moron, and that he had gone his whole 17 years without knowing his Father, it makes sense to assume that telling Squall that he was his father is what he wanted to talk about.
The blood evidence alone shows that Squall and Laguna are blood-relatives, and with the over evidence in mind, Squall is certainly Laguna and Raine's son.