There are 2 universes, this has been consistent throughout the entire series (so far). There are three universes, but one of them was only seen for a couple of scenes in 1x19, The Road Not Taken. Olivia witnesses the activation of the spontaneous-combustion twins in another universe, but not the one commonly referred to as "Over There" - in this one, the twins got activated at the same time, meaning they were indeed also treated with Cortexiphan. This universe was never revisited.
As for timelines:
- Seasons 1-3 are one timeline.
- In 3x22, The Day We Died, we get a glimpse at a second timeline - this is actually the "original" timeline, and shows how the machine got buried in the past of the Seasons 1-3 timeline.
- Season 4 (and so far in 5), is a third timeline.
- The Observers come from the future of a timeline that, seemingly, no longer exists. In 4x14, The End Of All Things, September mentions what should have happened (from their perspective of the past), and how he accidentally made it deviate. He also mentions at that time that the Observers have technology that allows them to exist outside of time, and that from our perspective, they are only one possible future.
So, 3 universes (so far, and one was only seen for a few moments in Season 1) and 3, maybe 4, timelines (so far).