There will definitly be a season 5. Atlantis is going way too good to stop. They are even already written:
Episode 1: Search and Rescue (II) SPOILERS:
Captain Alicia Vega, a 28-year-old new addition to Atlantis, speaks with Colonel Carter about her lack of an assignment. When the Stargate activates, the two rush down the stairs to meet Lt. Edison. Edison has rushed back from Michael's compound, where a number of Atlantis personnel are now trapped. He has come for back-up and to secure rescue for his team and the others.
Carter and Vega, joined by Dr. Keller and a contingent, gear up and head to the planet in a cloaked Jumper. They begin searching for their missing people -- including McKay and Lorne, who find themselves trapped together with no way out. But the team is being watched from overhead: Michael is on board a cruiser orbiting the planet, scanning their life signs. When he determines that the Atlantians are there and may still prove useful to his agenda, he launches Wraith Darts to capture them.
The search team falls back to their Jumper to wait for reinforcements, but it's too late to use the Stargate: the Wraith have dialed into the planet, preventing their escape. Now they, like their missing friends, are trapped.
Note: The name Alison Porter has been changed to Alicia Vega.
American premiere date unknown.
Episode 2: The Seed
Episode 3: Broken Ties
Episode 4: The Deadalus variations
Episode 5: Whispers
Episode 6: Amort
Episode 7: Ghost in the Machine
Episode 8: Tracker
Episode 9: The Queen