The two sets of pods came to Earth in the ship that crashed in 1947 and taken by the Army. They were in some kind of casing (perhaps to protect them on the journey) and it appears that the Army cut away the outer casing on one pod, and it was leaking some kind of fluid.
It is never said exactly, but it is generally believed that Nadeso put the pods in the pod chamber after they were rescued from the Army. At some time, the pods were removed from their casing, seperated and mounted on the wall of the pod chamber, while the other set was taken to New York and mounted on the wall in an unused subway track
As far as we know, the pods stayed in the chamber until they 'hatched' sometime in 1989.
Max tells Liz in the epi 'Balance' what he remembers about coming out of the pods.
I remember the first time I saw Michael. It was in the desert the night we first came out of the pods. The sky was bright with stars and this full moon. Isabel and I found each other first. We didn't know how to speak, but we could communicate anyway. We walked for a while, but we could both feel someone else.
He said he saw us, but that he was afraid. So he just watched us for a long time. When he finally revealed himself, he was standing on this rock. Just like you'd expect from Michael. "Here I am. Deal with me." He said it was the hardest thing he's ever had to do...to trust us.
Both Max and Isabel talk about when they came out of the pods at different times, but neither mentions a fourth pod nor Tess.
Later, Tess 'helps' Max remember her being in the pod, and it is a bit different than what he remembered.
Max remembers coming out of the pod and seeing Isabel and Michael already out. He sees Tess still in her pod. Michael moves to the door and opens it to leave. Isabel wants to leave too, and holds out a hand to Max, but he hesitates, looking to Tess in her pod, but eventually takes Isabel's hand and they go, leaving Tess still in her pod.
Perhaps Max just doesn't remember that part later, or perhaps Tess used her powers to make him remember what she wanted.
Early or Late Hatching?
Tess tells Max that Nasedo was there for her when she came out of her pod, so you have to wonder, why he wasn't there for the other three?
Was he late for some reason? Or did Max, Michael and Isabel come out of their pods early?
Or if you are partial to conspiracy theories, perhaps Nasedo wasn't there because he wasn't their protector and only found out about the pod chamber later.
Check here for info on the 'Leaky Pod Theory'