We cannot say it is canon or it isn't canon. But here are some things to consider when speculating...
1. In the original two fallout games, aliens were just Easter eggs for the player to laugh about it and go about their day as usual. In New Vegas, you can clearly see a crashed Mothership Zeta recon ship but again, it's an Easter egg, just like every Wild Wasteland encounter. Before Mothership Zeta, Fallout 3 had the famous Recon Ship Easter egg and the Firelance random encounter...and a mention of the former in the Citadel terminal. No game had a fleshed out DLC like Zeta.
2. Mothership Zeta did have more than a few references to Pre-War America, meaning it isn't really breaking lore. In regards to the aliens transmitting launch codes to U.S and Chinese missiles, it's only speculation and is completely proved false when you see somebody like Mr. House able to predict the political tensions of 2077 rather than putting aliens into his equations.
3. Not all decisions made by the player are canon, especially regarding decisions in the original game about Shady Sands. However, every main game and their DLC options ARE canon in some way. By main game, I mean the first two games by Interplay, Fallout 3 by Bethesda, and Fallout New Vegas by Obsidian. With that said, let's see all of the Fallout 3 DLC options.
Operation Anchorage is canon in terms of how the Anchorage battle played out(not to the letter of course as it is a simulation made by General Chase). The Pitt is kind of iffy but it is canon in terms of what the Pitt became after the Brotherhood scourge but before the Lone Wanderer came in. After that, it's really hard to tell. Broken Steel of course is canon and the canon option obviously is the Brotherhood of Steel knights are drinking mead in Camelot while the evil wizards of the Enclave are vanquished by a knight in shining armor. Point Lookout is...just a fun DLC. But it does reveal something about punga fruits and the state of the location where Point Lookout is.
Now for New Vegas DLC so far. Dead Money gives backstory on Father Elijah, Christine, and adds the Sierra Madre in the lore. Honest Hearts is the canon story about the Burned Man, and Old World Blues is the most epic rendition of what was happening in Pre-War America and adds to Ulysses' backstory along with building up for the final battle of epicosity with Ulysses.
So obviously every DLC is canon in some way and I think Mothership Zeta, being as linear as it is, is probably canon to a point. Except the Death Ray. I really can't see the Death Ray battle with the other ship at the end becoming canon as it pretty much gives the Lone Wanderer more power than any other protagonist. Yes, even the Courier. But I'm glad Mothership Zeta was created...why? Because it gave way for the most epic mod ever in Fallout 3. Mothership Zeta Crew