Unless you are targeting low end graphic cards it should be fine, though will eat up a fair amount of memory (16mb*6 = 96mb + mipmapping) unless they are compressed. So in this case i'd be more wary of memory useage/requirements than performance. Can you not drop down to 1024x1024? That could reduce memory by 75% (4mb*6 = 24mb+mipmaps)
There are other solutions such as using a different mapping such as spherical (on a sphere obviously), which from memory can potentially half the amount of memory you use on a cubemap with little loss in quality. HDR Shop can be useful for converting different mapping schemes if its still available.
Alternatively you could take the approach of mapping a bounding sphere or skybox. That is you create a mesh that allows you to place elements from a texture atlas or simply assign vertex colours or both. This is what HomeWorld did many years ago and there used to be a good webpage about it, but google is coming up empty.
You might also want to check out the inspirational Journal of Ysaneya for the Infinity game/engine he did some great stuff with nebulas and skyboxes. At one point these were just 1024x1024
Edit: Found a page about Homeworld backgrounds here
