Outside of the Metroid Queen, Omega Metroids will be the strongest the species has to offer. And yes, they will be difficult to defeat. Luckily, you can hit these guys in the mouth, which is a much larger hitbox than a Zeta Metroid's head. You can even go for its abdomen, but much like Zeta Metroids, you won't see many opportunities to do that. Missiles, Super Missiles and Ice Beams all work well on Omega Metroids.
Omega Metroids also have a variety of ways of attacking you. The first will be seen by it smacking its tail against the ground, causing rocks from above to start falling. Instead of trying to dodge all of them, shooting and destroying them works better. Plus, you'll get Health and Ammo for breaking the rocks. If the Omega Metroid does this while fire is on the ground - which will happen at some point to you - you'll have to resort to dodging the rocks. Use your Screw Attack when this does.
If one of them being to crouch, then it's going to leap Samus and try to crush you. Simply move back to avoid them. If one of their mouths begin to glow, it will shoot out a fire laser. If it's a normal laser, jump to avoid it. If the laser moves up and down - as it will sometimes do - Top Jump to the other side of the Metroid. Don't get too close to it though, as it will try to swipe at Samus if you do.
At one point, Zeta Metroids are bound to attempt to bite you. This will be seen when it head starts to glow a whitish color. When this happens and its head starts to glow, do a Melee Counter. If done properly, Samus will do a nice flip that opens the Zeta Metroid up for an attack. If you have some, this is the perfect opportunity to release one of your Super Missiles to cause maximum damage.