Yes, you can check at any level. But the reason Lv50 is better is because IV calculators will give you a range of possible IVs, unless it is level 100. Level 50 has a 2-value range, so is small enough to give you a more accurate answer. At Lv5, the range can be really big.
What I do to calculate Lv5 IVs, I see the range at level 5, I give it one rare candy, and use my IV calculator again, and see where the new range overlaps. I do this over again until it gets to one value. Of course, I saved before all this, so I can just turn it off again, so its level isn't affected, and I can train it right.