Left eye. And I'm right handed. I understand the benefits of using the right eye, but it just doesn't work for me.
My natural tendency is to close my right eye. But if I do this too much, I end up with a sore eyes and a headache. Ultimately, the view from both eyes won't align for a period of time. No idea why. I have to consciously will myself to keep both eyes open.
This problem I had, too. Until I switched from a 40D to full-frame 5D MkII. The 7D has enough viewfinder magnification that it almost appears as a FF viewfinder, so no problem there.
5D3, 5D2, Sony α6000, G16 | SY14 f/2.8, Ʃ20 f/1.8, 24 f/2.8, 35 f/2, Ʃ35 f/1.4A, 50 f/1.8 I, Ʃ50 f/1.4 EX, 100L Macro, 17-40L, 24-105L, 70-200 f/2.8L IS II, 1.4x II, 70-300L, 100-400L | E-mount: SY12 f/2, Ʃ19 & 30 f/2.8 EX DN, 16-70 ZA OSS, 55-210 OSS, Metabones SB | FT-QL, AE-1P | FD(n) & FL lenses