Psalm 121:1 I will lift up my eyes to the mountains; From where shall my help come?
Psalm 123:1 To you lift I up my eyes, O you that dwell in the heavens.
"He who previously lifted his eyes unto the hills, now hath raised his heart's eyes to the Lord Himself"--The Venerable Bede (8th century English monk)
Even if heaven isn't a physical place in the sky, if one is going to "look" somewhere while praying, I think up to the sky is as good a place as any. It's certainly more awe-inspiring and grand than looking in a bowl of soup (though God can be there too.) I do it myself, especially if I'm outside on a starry night.
I think Bede makes a good point about the psalmist: it is the heart's eyes that are being raised to the Lord. There is a physical, outward expression of the eyes looking "up", but that's not the point of the exercise. The point is that it's an act of submission, an acknowledgment that God is the source of our being and our help. Maybe the writer included this for the reader's benefit more than anything. Jesus certainly knew the Father wasn't floating up in the sky, but it sounds better and more poetic to include lifting up his eyes to heaven...Or perhaps he lifted his eyes up (if he literally did so at all) for the benefit of his disciples, if they were still around.