If there's a nice FA who's paid us a little attention (helping get settled, cooing over DS, talking about their baby, etc), I usually feel ok asking them to help if they're standing around in the area (i.e. not in the middle of beverage service). If not, I take him with me and hold him while I go. Not ideal, and not easy, but these are things that you learn to do when you have a baby. If I can nurse and go to the bathroom at the same time, going to the bathroom and just holding the baby isn't that hard.

If you're taking a sling or other baby carrier (like a Bjorn), you could strap baby on to free your hands up a little. I honestly think this problem is easier than trying to change squirmy baby's diaper on the toilet seat in the lav when the plane doesn't have a changing pad!