Hi, you were spot on. I stopped by an auto upholstery shop and spoke to the owner, showing him the pics above in an iPad and even brought the window with me. He described the process as you suggested, including removing the foam in order to add a washer to the inside of where the bigger hole is. There's about 3" of foam that I'll have to remove but doesn't seem to be too bad, as access to it isn't bad.
He said I could just buy a riveting tool and offered to sell me the snaps for a few bucks but I think I'll just bring them the boat and let them do the install as the cost would be virtually the same if I were to buy the material (around 30 bux). He also said I should remove the snaps that are loose as these will eventually fail. I don't have a metal drill bit so I may just let them handle this, as there are only 3 loose ones on the opposite side of the boat. For the low cost of repairing these, might as well let the experts handle it. I realize that not much skill is needed to install rivets but well, I'd only have one chance to get it right as I don't want to wreck the fiberglass. For the low cost, why not. They're close to home anyway.
For anyone searching this site for replacing broken/missing snaps, try to pay a visit to a local auto upholstery shop. Thanks for the reply above.